From 0630a86ecb9a4b99e84421bed6df1c3cb7fbb208 Mon Sep 17 00:00:00 2001
From: github-actions <github-actions@github.com>
Date: Wed, 12 Jun 2024 04:10:59 +0000
Subject: [PATCH] Updated the data.yml sourced from
 australianbiocommons.github.io

---
 _data/data.yaml | 6045 ++++++++++++++++-------------------------------
 1 file changed, 2099 insertions(+), 3946 deletions(-)

diff --git a/_data/data.yaml b/_data/data.yaml
index 8d5faa4..5b51cee 100644
--- a/_data/data.yaml
+++ b/_data/data.yaml
@@ -5,19 +5,13 @@
   description: 3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using
     HiC.
   edam-operations:
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: DNA
-    url: http://edamontology.org/topic_0654
+  - Scaffolding
+  - De-novo assembly
+  - Genome assembly
+  edam-topics:
+  - Sequence assembly
+  - Mapping
+  - DNA
   galaxy: ''
   homepage: https://github.com/aidenlab/3d-dna
   id: 3d-dna
@@ -40,13 +34,10 @@
   description: Mass screening of contigs for antimicrobial resistance or virulence
     genes.
   edam-operations:
-  - term: Antimicrobial resistance prediction
-    url: http://edamontology.org/operation_3482
+  - Antimicrobial resistance prediction
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Microbiology
-    url: http://edamontology.org/topic_3301
+  - Genomics
+  - Microbiology
   galaxy:
   - description: 'ABRicate List: List all of abricate''s available databases.'
     title: ABRicate List 1.0.1
@@ -75,15 +66,11 @@
   bunya: ''
   description: De novo genome sequence assembler using short reads.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
+  - Genome assembly
+  - De-novo assembly
+  - Scaffolding
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'ABySS: de novo sequence assembler'
     title: ABySS 2.3.7+galaxy0
@@ -113,13 +100,10 @@
     and a package of molecular simulation programs which includes source code and
     demos.'
   edam-operations:
-  - term: Modelling and simulation
-    url: http://edamontology.org/operation_2426
+  - Modelling and simulation
   edam-topics:
-  - term: Molecular modelling
-    url: http://edamontology.org/topic_2275
-  - term: Computational biology
-    url: http://edamontology.org/topic_3307
+  - Molecular modelling
+  - Computational biology
   galaxy:
   - description: 'Generate MD topologies for small molecules: using acpype'
     title: Generate MD topologies for small molecules 21.10+galaxy0
@@ -151,13 +135,10 @@
     itself. The suite can also be used to carry out complete (non-periodic) molecular
     dynamics simulations (using NAB), with generalized Born solvent models.
   edam-operations:
-  - term: Molecular dynamics simulation
-    url: http://edamontology.org/operation_2476
+  - Molecular dynamics simulation
   edam-topics:
-  - term: Molecular modelling
-    url: http://edamontology.org/topic_2275
-  - term: Molecular dynamics
-    url: http://edamontology.org/topic_0176
+  - Molecular modelling
+  - Molecular dynamics
   galaxy:
   - description: 'MMPBSA/MMGBSA: tool for estimating ligand binding affinities'
     title: MMPBSA/MMGBSA 21.10+galaxy0
@@ -185,17 +166,12 @@
     \ methods in different ways, to reveal information about codon context, codon\
     \ usage, nucleotide repeats within open reading frames (ORFeome) and others."
   edam-operations:
-  - term: Statistical inference
-    url: http://edamontology.org/operation_3658
-  - term: Nucleic acid sequence analysis
-    url: http://edamontology.org/operation_2478
-  - term: Coding region prediction
-    url: http://edamontology.org/operation_0436
-  edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
+  - Statistical inference
+  - Nucleic acid sequence analysis
+  - Coding region prediction
+  edam-topics:
+  - DNA
+  - Gene expression
   galaxy: ''
   homepage: http://bioinformatics.ua.pt/software/anaconda/
   id: anaconda
@@ -251,8 +227,7 @@
     be found at the Bioconductor website, for example, information on the human annotation
     package (org.Hs.eg.db) can be found here.
   edam-operations:
-  - term: Annotation
-    url: http://edamontology.org/operation_0226
+  - Annotation
   edam-topics: ''
   galaxy:
   - description: 'annotateMyIDs: annotate a generic set of identifiers'
@@ -277,17 +252,12 @@
     and cross-links with a large number of in silico secondary metabolite analysis
     tools that have been published earlier.
   edam-operations:
-  - term: Sequence clustering
-    url: http://edamontology.org/operation_0291
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
-  - term: Differential gene expression analysis
-    url: http://edamontology.org/operation_3223
+  - Sequence clustering
+  - Gene prediction
+  - Differential gene expression analysis
   edam-topics:
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
-  - term: Gene and protein families
-    url: http://edamontology.org/topic_0623
+  - Molecular interactions, pathways and networks
+  - Gene and protein families
   galaxy:
   - description: 'Antismash: allows the genome-wide identification, annotation and
       analysis of secondary metabolite biosynthesis gene clusters'
@@ -320,15 +290,11 @@
   - 0.4.2-gcccore-10.3.0
   description: Convert various sequence formats to FASTA
   edam-operations:
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  - term: Sequence conversion
-    url: http://edamontology.org/operation_0233
+  - Formatting
+  - Sequence conversion
   edam-topics:
-  - term: Data quality management
-    url: http://edamontology.org/topic_3572
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Data quality management
+  - Genomics
   galaxy: ''
   homepage: https://github.com/tseemann/any2fasta
   id: any2fasta
@@ -348,23 +314,15 @@
     to explore genomic annotations at many levels of detail, and to perform expert
     annotation curation, all in a graphical environment.
   edam-operations:
-  - term: Editing
-    url: http://edamontology.org/operation_3096
-  - term: Sequence annotation
-    url: http://edamontology.org/operation_0361
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  edam-topics:
-  - term: Data submission, annotation and curation
-    url: http://edamontology.org/topic_0219
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
+  - Editing
+  - Sequence annotation
+  - Genome annotation
+  edam-topics:
+  - Data submission, annotation and curation
+  - Gene transcripts
+  - Genomics
+  - Mapping
+  - Molecular interactions, pathways and networks
   galaxy: ''
   homepage: http://apollo.berkeleybop.org
   id: apollo
@@ -384,13 +342,10 @@
   bunya: ''
   description: ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
+  - Gene prediction
   edam-topics:
-  - term: Functional, regulatory and non-coding RNA
-    url: http://edamontology.org/topic_0659
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Functional, regulatory and non-coding RNA
+  - Genomics
   galaxy:
   - description: 'tRNA and tmRNA: prediction (Aragorn)'
     title: tRNA and tmRNA 0.6
@@ -435,17 +390,12 @@
     and truncations of genes (i.e., breakpoints in introns and intergenic regions).
     Arriba is the winner of the DREAM SMC-RNA Challenge.
   edam-operations:
-  - term: Structural variation detection
-    url: http://edamontology.org/operation_3228
-  - term: Split read mapping
-    url: http://edamontology.org/operation_3199
+  - Structural variation detection
+  - Split read mapping
   edam-topics:
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: RNA splicing
-    url: http://edamontology.org/topic_3320
-  - term: DNA structural variation
-    url: http://edamontology.org/topic_3175
+  - Gene transcripts
+  - RNA splicing
+  - DNA structural variation
   galaxy:
   - description: 'Arriba: detect gene fusions from STAR aligned RNA-Seq data'
     title: Arriba 2.4.0+galaxy1
@@ -478,13 +428,10 @@
     as input to find new members of the family in a genome. It can be run through
     a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
+  - Gene prediction
   edam-topics:
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: Gene and protein families
-    url: http://edamontology.org/topic_0623
+  - Gene transcripts
+  - Gene and protein families
   galaxy:
   - description: 'Augustus: gene prediction for prokaryotic and eukaryotic genomes'
     title: Augustus 3.4.0+galaxy1
@@ -533,15 +480,11 @@
     docking and virtual screening, offering multi-core capability, high performance
     and enhanced accuracy and ease of use.
   edam-operations:
-  - term: Molecular docking
-    url: http://edamontology.org/operation_0478
+  - Molecular docking
   edam-topics:
-  - term: Drug discovery
-    url: http://edamontology.org/topic_3336
-  - term: Molecular modelling
-    url: http://edamontology.org/topic_2275
-  - term: Molecular docking
-    url: http://edamontology.org/topic_2275
+  - Drug discovery
+  - Molecular modelling
+  - Molecular docking
   galaxy:
   - description: 'Prepare ligand: for docking with Autodock Vina'
     title: Prepare ligand 1.5.7+galaxy0
@@ -576,15 +519,11 @@
   bunya: ''
   description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Genome annotation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Data submission, annotation and curation
-    url: http://edamontology.org/topic_0219
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Genomics
+  - Data submission, annotation and curation
+  - Sequence analysis
   galaxy:
   - description: 'Bakta: Genome annotation via alignment-free sequence identification'
     title: Bakta 1.9.2+galaxy0
@@ -610,17 +549,12 @@
   description: BamTools provides a fast, flexible C++ API & toolkit for reading, writing,
     and managing BAM files.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Sequence alignment analysis
-    url: http://edamontology.org/operation_0258
+  - Data handling
+  - Sequence alignment analysis
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Data management
-    url: http://edamontology.org/topic_3071
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequencing
+  - Data management
+  - Sequence analysis
   galaxy:
   - description: 'Split BAM by read tag value: into a dataset list collection'
     title: Split BAM by read tag value 2.5.2+galaxy2
@@ -651,11 +585,9 @@
   bunya: ''
   description: Bamutil provides a serie of programs to work on SAM/BAM files.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Data management
   galaxy:
   - description: 'BamUtil diff: two coordinate sorted SAM/BAM files'
     title: BamUtil diff 1.0.15+galaxy1
@@ -681,13 +613,10 @@
     made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises
     assembly graphs, with connections, using graph layout algorithms.
   edam-operations:
-  - term: Sequence assembly visualisation
-    url: http://edamontology.org/operation_3184
+  - Sequence assembly visualisation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Genomics
+  - Sequence assembly
   galaxy:
   - description: 'Bandage Info: determine statistics of de novo assembly graphs'
     title: Bandage Info 2022.09+galaxy2
@@ -715,15 +644,11 @@
     bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes
     (5S,5.8S,28S,18S).
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
+  - Gene prediction
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
+  - Genomics
+  - Model organisms
+  - Model organisms
   galaxy:
   - description: 'barrnap: Locate ribosomal RNA''s in a fasta file. (GFF output)'
     title: barrnap 1.2.2
@@ -767,31 +692,19 @@
     than almost all short-read aligners, yet retains unrivaled sensitivity and specificity,
     particularly for reads with many errors and indels.
   edam-operations:
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
-  - term: Sequence contamination filtering
-    url: http://edamontology.org/operation_3187
-  - term: Read binning
-    url: http://edamontology.org/operation_3798
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: RNA splicing
-    url: http://edamontology.org/topic_3320
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - RNA-Seq analysis
+  - Sequence trimming
+  - Read mapping
+  - Sequence contamination filtering
+  - Read binning
+  - Sequence alignment
+  edam-topics:
+  - Sequencing
+  - RNA splicing
+  - Whole genome sequencing
+  - Phylogenetics
+  - Metagenomics
+  - RNA-Seq
   galaxy:
   - description: 'BBTools: BBduk: decontamination using kmers'
     title: 'BBTools: BBduk 39.06+galaxy2'
@@ -816,10 +729,8 @@
     by rebasing some analysis results against the parent features which were originally
     analysed.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Data handling
+  - Formatting
   edam-topics: ''
   galaxy:
   - description: 'Rebase GFF3 features: against parent features'
@@ -854,19 +765,13 @@
     Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently
     with both VCFs and BCFs, both uncompressed and BGZF-compressed.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
+  - Data handling
+  - Variant calling
   edam-topics:
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: GWAS study
-    url: http://edamontology.org/topic_3517
-  - term: Genotyping experiment
-    url: http://edamontology.org/topic_3516
+  - Genetic variation
+  - DNA polymorphism
+  - GWAS study
+  - Genotyping experiment
   galaxy:
   - description: 'bcftools annotate: Annotate and edit VCF/BCF files'
     title: bcftools annotate 1.15.1+galaxy3
@@ -1018,13 +923,10 @@
   description: Beagle is a software package that performs genotype calling, genotype
     phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
   edam-operations:
-  - term: Phasing
-    url: http://edamontology.org/operation_3454
-  - term: Imputation
-    url: http://edamontology.org/operation_3557
+  - Phasing
+  - Imputation
   edam-topics:
-  - term: Population genetics
-    url: http://edamontology.org/topic_3056
+  - Population genetics
   galaxy: ''
   homepage: https://faculty.washington.edu/browning/beagle/beagle.html
   id: beagle
@@ -1054,17 +956,12 @@
   description: BEAGLE is a high-performance library that can perform the core calculations
     at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
   edam-operations:
-  - term: Phylogenetic inference
-    url: http://edamontology.org/operation_0323
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Phylogenetic inference
+  - Standardisation and normalisation
+  edam-topics:
+  - Phylogenetics
+  - Statistics and probability
+  - Computer science
   galaxy: ''
   homepage: https://github.com/beagle-dev/beagle-lib
   id: beagle-lib
@@ -1091,17 +988,12 @@
     of reconstructing phylogenies but is also a framework for testing evolutionary
     hypotheses without conditioning on a single tree topology.
   edam-operations:
-  - term: Multiple sequence alignment
-    url: http://edamontology.org/operation_0492
-  - term: Phylogenetic tree generation (from molecular sequences)
-    url: http://edamontology.org/operation_0540
-  - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
-    url: http://edamontology.org/operation_0547
-  edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Multiple sequence alignment
+  - Phylogenetic tree generation (from molecular sequences)
+  - Phylogenetic tree generation (maximum likelihood and Bayesian methods)
+  edam-topics:
+  - Phylogenetics
+  - Sequence analysis
   galaxy: ''
   homepage: http://beast.bio.ed.ac.uk/
   id: beast
@@ -1134,15 +1026,11 @@
     user-interface for setting up standard analyses and a suit of programs for analysing
     the results.
   edam-operations:
-  - term: Phylogenetic tree reconstruction
-    url: http://edamontology.org/operation_3478
-  - term: Phylogenetic tree analysis (shape)
-    url: http://edamontology.org/operation_0551
+  - Phylogenetic tree reconstruction
+  - Phylogenetic tree analysis (shape)
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
+  - Phylogenetics
+  - Phylogenomics
   galaxy: ''
   homepage: http://www.beast2.org
   id: beast2
@@ -1164,11 +1052,9 @@
   description: Convert a BED format file of the proteins from a proteomics search
     database into a tabular format for the Multiomics Visualization Platform (MVP).
   edam-operations:
-  - term: Conversion
-    url: http://edamontology.org/operation_3434
+  - Conversion
   edam-topics:
-  - term: Literature and language
-    url: http://edamontology.org/topic_3068
+  - Literature and language
   galaxy:
   - description: 'bed to protein map: genomic location of proteins for MVP'
     title: bed to protein map 0.2.0
@@ -1213,11 +1099,9 @@
   description: BEDTools is an extensive suite of utilities for comparing genomic features
     in BED format.
   edam-operations:
-  - term: Mapping
-    url: http://edamontology.org/operation_2429
+  - Mapping
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy:
   - description: 'bedtools GroupByBed: group by common cols and summarize other cols'
     title: bedtools GroupByBed 2.30.0
@@ -1385,25 +1269,16 @@
     The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon).
     This is recommended, as it avoids backwards compatibility problems with TransRate'
   edam-operations:
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Validation
-    url: http://edamontology.org/operation_2428
-  - term: de Novo sequencing
-    url: http://edamontology.org/operation_3644
-  - term: Transcriptome assembly
-    url: http://edamontology.org/operation_3258
-  - term: Chimera detection
-    url: http://edamontology.org/operation_0450
-  edam-topics:
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - De-novo assembly
+  - Validation
+  - de Novo sequencing
+  - Transcriptome assembly
+  - Chimera detection
+  edam-topics:
+  - Transcriptomics
+  - Sequence assembly
+  - RNA-Seq
+  - Workflows
   galaxy:
   - description: 'Filter and merge: chimeric reads from Arima Genomics'
     title: Filter and merge 1.0+galaxy1
@@ -1427,13 +1302,10 @@
   bunya: ''
   description: Trim, circularise, orient and filter long read bacterial genome assemblies
   edam-operations:
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
+  - Filtering
+  - Sequence trimming
   edam-topics:
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Computer science
   galaxy:
   - description: 'Berokka: Trim, circularise, orient and filter long read bacterial
       genome assemblies'
@@ -1500,23 +1372,15 @@
   description: Bio3D is an R package containing utilities for the analysis of protein
     structure, sequence and trajectory data.
   edam-operations:
-  - term: Essential dynamics
-    url: http://edamontology.org/operation_3891
-  - term: Molecular dynamics
-    url: http://edamontology.org/operation_2476
-  - term: Protein structure analysis
-    url: http://edamontology.org/operation_2406
-  - term: Principal component visualisation
-    url: http://edamontology.org/operation_2939
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  edam-topics:
-  - term: Structure analysis
-    url: http://edamontology.org/topic_0081
-  - term: Gene and protein families
-    url: http://edamontology.org/topic_0623
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
+  - Essential dynamics
+  - Molecular dynamics
+  - Protein structure analysis
+  - Principal component visualisation
+  - Sequence trimming
+  edam-topics:
+  - Structure analysis
+  - Gene and protein families
+  - Bioinformatics
   galaxy:
   - description: 'PCA: - principal component analysis using Bio3D'
     title: PCA 2.3.4
@@ -1569,11 +1433,9 @@
   description: Tools for early stage NGS alignment file processing including fast
     sorting and duplicate marking.
   edam-operations:
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
+  - Filtering
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Sequencing
   galaxy: ''
   homepage: http://www.sanger.ac.uk/science/tools/biobambam
   id: biobambam
@@ -1618,13 +1480,10 @@
     but with a decidedly "R flavor" that should be familiar to R users. This includes
     S4 classes and methods, as well as extensions of common core functions/methods.
   edam-operations:
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Formatting
   edam-topics:
-  - term: Laboratory information management
-    url: http://edamontology.org/topic_0607
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Laboratory information management
+  - Sequence analysis
   galaxy:
   - description: 'Convert: between BIOM table formats'
     title: Convert 2.1.15+galaxy1
@@ -1675,17 +1534,12 @@
     scripts for bioinformatics applications.  It provides software modules for many
     of the typical tasks of bioinformatics programming.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Service invocation
-    url: http://edamontology.org/operation_3763
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Software engineering
-    url: http://edamontology.org/topic_3372
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Data handling
+  - Service invocation
+  edam-topics:
+  - Genomics
+  - Software engineering
+  - Data management
   galaxy: ''
   homepage: http://bioperl.org/
   id: bioperl
@@ -1708,23 +1562,15 @@
   description: Biopython is a set of freely available tools for biological computation
     written in Python by an international team of developers.
   edam-operations:
-  - term: Deposition
-    url: http://edamontology.org/operation_3431
-  - term: Service invocation
-    url: http://edamontology.org/operation_3763
-  - term: Query and retrieval
-    url: http://edamontology.org/operation_0224
-  - term: Aggregation
-    url: http://edamontology.org/operation_3436
-  edam-topics:
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
-  - term: Data management
-    url: http://edamontology.org/topic_3071
-  - term: Software engineering
-    url: http://edamontology.org/topic_3372
-  - term: Computational biology
-    url: http://edamontology.org/topic_3307
+  - Deposition
+  - Service invocation
+  - Query and retrieval
+  - Aggregation
+  edam-topics:
+  - Bioinformatics
+  - Data management
+  - Software engineering
+  - Computational biology
   galaxy:
   - description: 'Translate BED transcripts: cDNA in 3frames or CDS'
     title: Translate BED transcripts 0.1.0
@@ -1758,23 +1604,15 @@
   description: BioTransformer is a freely available web server that supports accurate,
     rapid and comprehensive in silico metabolism prediction.
   edam-operations:
-  - term: Metabolic pathway prediction
-    url: http://edamontology.org/operation_3929
-  - term: PTM site prediction
-    url: http://edamontology.org/operation_0417
-  - term: Natural product identification
-    url: http://edamontology.org/operation_3803
-  edam-topics:
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
-  - term: Endocrinology and metabolism
-    url: http://edamontology.org/topic_3407
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
-  - term: Carbohydrates
-    url: http://edamontology.org/topic_0152
-  - term: NMR
-    url: http://edamontology.org/topic_0593
+  - Metabolic pathway prediction
+  - PTM site prediction
+  - Natural product identification
+  edam-topics:
+  - Small molecules
+  - Endocrinology and metabolism
+  - Metabolomics
+  - Carbohydrates
+  - NMR
   galaxy:
   - description: 'BioTransformer: '
     title: BioTransformer 3.0_20230403+galaxy1
@@ -1799,19 +1637,13 @@
   description: Bismark is a tool to map bisulfite treated sequencing reads and perform
     methylation calling in a quick and easy-to-use fashion.
   edam-operations:
-  - term: Methylation analysis
-    url: http://edamontology.org/operation_3204
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
-  - term: Bisulfite mapping
-    url: http://edamontology.org/operation_3186
+  - Methylation analysis
+  - Read mapping
+  - Bisulfite mapping
   edam-topics:
-  - term: Epigenomics
-    url: http://edamontology.org/topic_3173
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Epigenetics
-    url: http://edamontology.org/topic_3295
+  - Epigenomics
+  - Genomics
+  - Epigenetics
   galaxy:
   - description: 'Bismark Deduplicate: Deduplicates reads mapped by Bismark'
     title: Bismark Deduplicate 0.22.1
@@ -1849,15 +1681,11 @@
     The program compares nucleotide or protein sequences to sequence databases and
     calculates the statistical significance.
   edam-operations:
-  - term: Sequence similarity search
-    url: http://edamontology.org/operation_0346
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence similarity search
+  - Sequence alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
+  - Sequence analysis
+  - Bioinformatics
   galaxy: ''
   homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
   id: blast
@@ -1892,15 +1720,11 @@
     The program compares nucleotide or protein sequences to sequence databases and
     calculates the statistical significance.
   edam-operations:
-  - term: Sequence similarity search
-    url: http://edamontology.org/operation_0346
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence similarity search
+  - Sequence alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
+  - Sequence analysis
+  - Bioinformatics
   galaxy:
   - description: 'NCBI BLAST+ segmasker: low-complexity regions in protein sequences'
     title: NCBI BLAST+ segmasker 2.14.1+galaxy2
@@ -1984,11 +1808,9 @@
   - 3.7-gcc-11.3.0
   description: Fast, accurate spliced alignment of DNA sequences.
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy: ''
   homepage: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
   id: blat
@@ -2009,11 +1831,9 @@
   bunya: ''
   description: detect blocks of overlapping reads using a gaussian-distribution approach
   edam-operations:
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
+  - RNA-Seq analysis
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy:
   - description: 'blockbuster: detects blocks of overlapping reads using a gaussian-distribution
       approach'
@@ -2082,15 +1902,11 @@
     support for tasks and structures such as linear algebra, pseudorandom number generation,
     multithreading, image processing, regular expressions, and unit testing.
   edam-operations:
-  - term: Image analysis
-    url: http://edamontology.org/operation_3443
+  - Image analysis
   edam-topics:
-  - term: Pure mathematics
-    url: http://edamontology.org/topic_3570
-  - term: Imaging
-    url: http://edamontology.org/topic_3382
-  - term: Software engineering
-    url: http://edamontology.org/topic_3372
+  - Pure mathematics
+  - Imaging
+  - Software engineering
   galaxy: ''
   homepage: https://www.boost.org/
   id: boost
@@ -2114,17 +1930,12 @@
   - 1.3.1-gcc-11.3.0
   description: Bowtie is an ultrafast, memory-efficient short read aligner.
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence alignment
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Mapping
+  - Genomics
+  - Sequencing
+  - Sequence assembly
   galaxy:
   - description: 'Bowtie2: - map reads against reference genome'
     title: Bowtie2 2.5.3+galaxy1
@@ -2163,15 +1974,11 @@
     footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end
     alignment modes.'
   edam-operations:
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
+  - Read mapping
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Mapping
+  - Genomics
+  - Mapping
   galaxy: ''
   homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
   id: bowtie2
@@ -2228,15 +2035,11 @@
   description: Pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET
     and AUGUSTUS.
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Genome annotation
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: RNA
-    url: http://edamontology.org/topic_0099
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - RNA-Seq
+  - RNA
+  - Workflows
   galaxy:
   - description: 'BRAKER3: genome annotation'
     title: BRAKER3 3.0.6+galaxy2
@@ -2260,15 +2063,11 @@
   bunya: ''
   description: Runs Breseq software on a set of fastq files.
   edam-operations:
-  - term: Polymorphism detection
-    url: http://edamontology.org/operation_3202
+  - Polymorphism detection
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: DNA mutation
-    url: http://edamontology.org/topic_2533
+  - Sequencing
+  - Sequence analysis
+  - DNA mutation
   galaxy:
   - description: 'breseq: find mutations in haploid microbial genomes'
     title: breseq 0.35.5+0
@@ -2301,23 +2100,15 @@
     set, and transcriptome completeness based on evolutionarily informed expectations
     of gene content from near-universal single-copy orthologs.
   edam-operations:
-  - term: Sequence assembly validation
-    url: http://edamontology.org/operation_3180
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Transcriptome assembly
-    url: http://edamontology.org/operation_3258
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence assembly validation
+  - Scaffolding
+  - Genome assembly
+  - Transcriptome assembly
+  edam-topics:
+  - Sequence assembly
+  - Genomics
+  - Transcriptomics
+  - Sequence analysis
   galaxy:
   - description: 'Busco: assess genome assembly and annotation completeness'
     title: Busco 5.5.0+galaxy0
@@ -2348,21 +2139,14 @@
   bunya: ''
   description: Accelerated nanopore basecalling with SLOW5 data format.
   edam-operations:
-  - term: Base-calling
-    url: http://edamontology.org/operation_3185
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  - term: Splitting
-    url: http://edamontology.org/operation_3359
-  edam-topics:
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
-  - term: Protein expression
-    url: http://edamontology.org/topic_0108
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
+  - Base-calling
+  - Formatting
+  - Splitting
+  edam-topics:
+  - Computer science
+  - Protein expression
+  - Workflows
+  - Transcription factors and regulatory sites
   galaxy: ''
   homepage: https://github.com/Psy-Fer/buttery-eel
   id: buttery-eel
@@ -2389,11 +2173,9 @@
   description: Fast, accurate, memory-efficient aligner for short and long sequencing
     reads
   edam-operations:
-  - term: Genome indexing
-    url: http://edamontology.org/operation_3211
+  - Genome indexing
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Mapping
   galaxy:
   - description: 'Map with BWA: - map short reads (< 100 bp) against reference genome'
     title: Map with BWA 0.7.17.5
@@ -2436,11 +2218,9 @@
     alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset
     and the running machine.
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence alignment
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Mapping
   galaxy:
   - description: 'BWA-MEM2: - map medium and long reads (> 100 bp) against reference
       genome'
@@ -2509,8 +2289,7 @@
     alignments.
   edam-operations: ''
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'Base Coverage: of all intervals'
     title: Base Coverage 1.0.0
@@ -2579,12 +2358,9 @@
     results
   edam-operations: ''
   edam-topics:
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Oncology
-    url: http://edamontology.org/topic_2640
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Genetic variation
+  - Oncology
+  - Sequencing
   galaxy:
   - description: 'Copernicus Climate Data Store: for retrieveing climate data'
     title: Copernicus Climate Data Store 0.1.0
@@ -2607,23 +2383,15 @@
   bunya: ''
   description: Cactus is a reference-free whole-genome multiple alignment program.
   edam-operations:
-  - term: Multiple sequence alignment
-    url: http://edamontology.org/operation_0492
-  - term: Genome alignment
-    url: http://edamontology.org/operation_3182
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
+  - Multiple sequence alignment
+  - Genome alignment
+  edam-topics:
+  - Genomics
+  - Sequence analysis
+  - Phylogeny
+  - Sequence assembly
+  - Mapping
+  - Phylogenetics
   galaxy:
   - description: 'Cactus: whole-genome multiple sequence alignment'
     title: Cactus 2.7.1+galaxy0
@@ -2658,11 +2426,9 @@
     isotopes and adducts, isotope validation, EIC correlation based tagging of unknown
     adducts and fragments.
   edam-operations:
-  - term: Sequence annotation
-    url: http://edamontology.org/operation_0361
+  - Sequence annotation
   edam-topics:
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Metabolomics
   galaxy:
   - description: 'CAMERA.annotate: CAMERA annotate function. Returns annotation results
       (isotope peaks, adducts and fragments) and a diffreport if more than one condition.'
@@ -2694,11 +2460,9 @@
   description: De-novo assembly tool for long read chemistry like Nanopore data and
     PacBio data.
   edam-operations:
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
+  - De-novo assembly
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy:
   - description: 'Canu assembler: Assembler optimized for long error-prone reads such
       as PacBio, Oxford Nanopore'
@@ -2728,23 +2492,15 @@
   bunya: ''
   description: Web-based contig assembly.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Mapping assembly
-    url: http://edamontology.org/operation_0523
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
+  - Genome assembly
+  - Mapping assembly
+  - Sequence assembly
+  - Scaffolding
+  edam-topics:
+  - Sequence assembly
+  - Sequencing
+  - Sequence analysis
+  - Genetic variation
   galaxy:
   - description: 'cap3: Sequence Assembly tool'
     title: cap3 2.0.0
@@ -2769,17 +2525,12 @@
     imaging datasets, including methods for efficient pre-processing, spatial segmentation,
     and classification.
   edam-operations:
-  - term: Spectral analysis
-    url: http://edamontology.org/operation_3214
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  - term: Mass spectra calibration
-    url: http://edamontology.org/operation_3627
+  - Spectral analysis
+  - Standardisation and normalisation
+  - Mass spectra calibration
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
+  - Proteomics
+  - Data visualisation
   galaxy:
   - description: 'MSI classification: spatial classification of mass spectrometry
       imaging data'
@@ -2834,21 +2585,14 @@
     classification of the entire contig / MAG based on classification of the individual
     ORFs.
   edam-operations:
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Coding region prediction
-    url: http://edamontology.org/operation_0436
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Metagenomic sequencing
-    url: http://edamontology.org/topic_3837
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Taxonomic classification
+  - Sequence assembly
+  - Coding region prediction
+  edam-topics:
+  - Metagenomics
+  - Metagenomic sequencing
+  - Taxonomy
+  - Sequence assembly
   galaxy:
   - description: 'CAT bins: annotate with taxonomic classification'
     title: CAT bins 5.0.3.1
@@ -2878,11 +2622,9 @@
   - 4.8.1-gcc-11.3.0                   (D)
   description: Cluster a nucleotide dataset into representative sequences.
   edam-operations:
-  - term: Sequence clustering
-    url: http://edamontology.org/operation_0291
+  - Sequence clustering
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Sequencing
   galaxy:
   - description: 'CD-HIT-EST: Cluster a nucleotide dataset into representative sequences'
     title: CD-HIT-EST 1.3
@@ -2919,15 +2661,11 @@
   description: celseq2 is a Python framework for generating the UMI count matrix from
     CEL-Seq2 sequencing data.
   edam-operations:
-  - term: Demultiplexing
-    url: http://edamontology.org/operation_3933
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
+  - Demultiplexing
+  - RNA-Seq analysis
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - RNA-Seq
+  - Transcriptomics
   galaxy: ''
   homepage: https://github.com/yanailab/celseq2
   id: celseq2
@@ -2948,19 +2686,13 @@
   description: Tool for quantifying data from biological images, particularly in high-throughput
     experiments.
   edam-operations:
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Image analysis
-    url: http://edamontology.org/operation_3443
-  - term: Parsing
-    url: http://edamontology.org/operation_1812
+  - Quantification
+  - Image analysis
+  - Parsing
   edam-topics:
-  - term: Imaging
-    url: http://edamontology.org/topic_3382
-  - term: Microarray experiment
-    url: http://edamontology.org/topic_3518
-  - term: Genotype and phenotype
-    url: http://edamontology.org/topic_0625
+  - Imaging
+  - Microarray experiment
+  - Genotype and phenotype
   galaxy:
   - description: 'TrackObjects: with CellProfiler'
     title: TrackObjects 3.1.9+galaxy1
@@ -3074,15 +2806,11 @@
     for single-cell transcriptomics datasets, such as those coming from the Human
     Cell Atlas.
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Essential dynamics
-    url: http://edamontology.org/operation_3891
+  - Visualisation
+  - Essential dynamics
   edam-topics:
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: Cell biology
-    url: http://edamontology.org/topic_2229
+  - Transcriptomics
+  - Cell biology
   galaxy:
   - description: 'Interactive CellXgene Environment: '
     title: Interactive CellXgene Environment 1.1.1
@@ -3108,29 +2836,18 @@
   description: CheckM provides a set of tools for assessing the quality of genomes
     recovered from isolates, single cells, or metagenomes.
   edam-operations:
-  - term: Sequence assembly validation
-    url: http://edamontology.org/operation_3180
-  - term: Validation
-    url: http://edamontology.org/operation_2428
-  - term: Sequence composition calculation
-    url: http://edamontology.org/operation_0236
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Data quality management
-    url: http://edamontology.org/topic_3572
+  - Sequence assembly validation
+  - Validation
+  - Sequence composition calculation
+  - Sequencing quality control
+  - Statistical calculation
+  edam-topics:
+  - Genomics
+  - Phylogenomics
+  - Phylogenetics
+  - Taxonomy
+  - Metagenomics
+  - Data quality management
   galaxy: ''
   homepage: https://ecogenomics.github.io/CheckM
   id: checkm
@@ -3153,29 +2870,18 @@
   description: CheckM provides a set of tools for assessing the quality of genomes
     recovered from isolates, single cells, or metagenomes.
   edam-operations:
-  - term: Sequence assembly validation
-    url: http://edamontology.org/operation_3180
-  - term: Validation
-    url: http://edamontology.org/operation_2428
-  - term: Sequence composition calculation
-    url: http://edamontology.org/operation_0236
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Data quality management
-    url: http://edamontology.org/topic_3572
+  - Sequence assembly validation
+  - Validation
+  - Sequence composition calculation
+  - Sequencing quality control
+  - Statistical calculation
+  edam-topics:
+  - Genomics
+  - Phylogenomics
+  - Phylogenetics
+  - Taxonomy
+  - Metagenomics
+  - Data quality management
   galaxy: ''
   homepage: https://ecogenomics.github.io/CheckM
   id: checkm-database
@@ -3198,15 +2904,11 @@
     bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted
     and curated from the primary scientific literature.
   edam-operations:
-  - term: Data retrieval
-    url: http://edamontology.org/operation_2422
+  - Data retrieval
   edam-topics:
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
-  - term: Chemical biology
-    url: http://edamontology.org/topic_3369
-  - term: Cheminformatics
-    url: http://edamontology.org/topic_2258
+  - Small molecules
+  - Chemical biology
+  - Cheminformatics
   galaxy:
   - description: 'Search ChEMBL database: for compounds which are similar to a SMILES
       string'
@@ -3247,21 +2949,14 @@
     an evaluation copy of the most recent version of chemfp, or you can download an
     earlier version for no cost under the MIT license'
   edam-operations:
-  - term: Database search
-    url: http://edamontology.org/operation_2421
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  edam-topics:
-  - term: Cheminformatics
-    url: http://edamontology.org/topic_2258
-  - term: Chemistry
-    url: http://edamontology.org/topic_3314
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
-  - term: Literature and language
-    url: http://edamontology.org/topic_3068
+  - Database search
+  - Standardisation and normalisation
+  - Formatting
+  edam-topics:
+  - Cheminformatics
+  - Chemistry
+  - Transcription factors and regulatory sites
+  - Literature and language
   galaxy:
   - description: 'Molecule to fingerprint: conversion to several different fingerprint
       formats'
@@ -3304,23 +2999,15 @@
     covering assembly of a compound library, hole filling, protein-ligand docking,
     and construction of a quantitative structure-activity relationship (QSAR) model.
   edam-operations:
-  - term: Protein-ligand docking
-    url: http://edamontology.org/operation_0482
-  - term: Molecular dynamics
-    url: http://edamontology.org/operation_2476
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  edam-topics:
-  - term: Cheminformatics
-    url: http://edamontology.org/topic_2258
-  - term: Molecular modelling
-    url: http://edamontology.org/topic_2275
-  - term: Compound libraries and screening
-    url: http://edamontology.org/topic_3343
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
+  - Protein-ligand docking
+  - Molecular dynamics
+  - Sequence assembly
+  edam-topics:
+  - Cheminformatics
+  - Molecular modelling
+  - Compound libraries and screening
+  - Workflows
+  - Small molecules
   galaxy:
   - description: 'Online data: fetching ...'
     title: Online data 0.2
@@ -3354,21 +3041,14 @@
     to compare the own dataset with those deposited in database. The comparison can
     be used to infer cooperative regulation and thus can be used to generate hypotheses.
   edam-operations:
-  - term: Sequence annotation
-    url: http://edamontology.org/operation_0361
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Gene-set enrichment analysis
-    url: http://edamontology.org/operation_2436
-  - term: Sequence feature comparison
-    url: http://edamontology.org/operation_0256
-  edam-topics:
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
-  - term: Data mining
-    url: http://edamontology.org/topic_3473
+  - Sequence annotation
+  - Visualisation
+  - Gene-set enrichment analysis
+  - Sequence feature comparison
+  edam-topics:
+  - ChIP-seq
+  - Data visualisation
+  - Data mining
   galaxy:
   - description: 'ChIPseeker: for ChIP peak annotation and visualization'
     title: ChIPseeker 1.28.3+galaxy0
@@ -3393,13 +3073,10 @@
   description: An ultra fast, heuristic approach to detect conserved signals in extremely
     large pairwise genome comparisons (dotplot).
   edam-operations:
-  - term: Dot plot plotting
-    url: http://edamontology.org/operation_0490
+  - Dot plot plotting
   edam-topics:
-  - term: Comparative genomics
-    url: http://edamontology.org/topic_0797
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Comparative genomics
+  - Sequence analysis
   galaxy:
   - description: 'Chromeister: ultra-fast pairwise genome comparisons'
     title: Chromeister 1.5.a+galaxy1
@@ -3463,13 +3140,10 @@
   description: Circos is tool for visualizing data in a circular format. It was developed
     for genomic data but can work for many other kinds of data as well.
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Visualisation
   edam-topics:
-  - term: Comparative genomics
-    url: http://edamontology.org/topic_0797
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
+  - Comparative genomics
+  - Data visualisation
   galaxy:
   - description: 'Circos: Interval to Circos Text Labels: reformats interval files
       to prepare for Circos text labels'
@@ -3598,21 +3272,14 @@
     clustermap.js is an interactive, reusable d3 chart designed to visualise homology
     between multiple gene clusters.'
   edam-operations:
-  - term: Sequence clustering
-    url: http://edamontology.org/operation_0291
-  - term: Sequence cluster visualisation
-    url: http://edamontology.org/operation_0566
-  - term: Dendrogram visualisation
-    url: http://edamontology.org/operation_2938
-  edam-topics:
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Imaging
-    url: http://edamontology.org/topic_3382
+  - Sequence clustering
+  - Sequence cluster visualisation
+  - Dendrogram visualisation
+  edam-topics:
+  - Molecular interactions, pathways and networks
+  - Sequence analysis
+  - Workflows
+  - Imaging
   galaxy:
   - description: 'clinker: Automatic creation of publication-ready gene cluster comparison
       figures'
@@ -3658,11 +3325,9 @@
   description: "Multiple sequence alignment software. The name is occassionally spelled\
     \ as ClustalOmega, Clustal \u03A9, Clustal\u03A9, Clustal O, ClustalO."
   edam-operations:
-  - term: Multiple sequence alignment
-    url: http://edamontology.org/operation_0492
+  - Multiple sequence alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy: ''
   homepage: http://www.clustal.org/omega/
   id: clustalo
@@ -3689,11 +3354,9 @@
   description: Multiple sequence alignment software. Old deprecated versions. Even
     older versions were CLUSTAL and CLUSTAL V (ClustalV).
   edam-operations:
-  - term: Multiple sequence alignment
-    url: http://edamontology.org/operation_0492
+  - Multiple sequence alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'ClustalW: multiple sequence alignment program for DNA or proteins'
     title: ClustalW 2.1+galaxy1
@@ -3729,23 +3392,15 @@
   description: ColabFold databases are MMseqs2 expandable profile databases to generate
     diverse multiple sequence alignments to predict protein structures.
   edam-operations:
-  - term: Database search
-    url: http://edamontology.org/operation_2421
-  - term: Protein structure prediction
-    url: http://edamontology.org/operation_0474
-  - term: Fold recognition
-    url: http://edamontology.org/operation_0303
-  edam-topics:
-  - term: Protein folds and structural domains
-    url: http://edamontology.org/topic_0736
-  - term: Protein folding, stability and design
-    url: http://edamontology.org/topic_0130
-  - term: Structure prediction
-    url: http://edamontology.org/topic_0082
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Database search
+  - Protein structure prediction
+  - Fold recognition
+  edam-topics:
+  - Protein folds and structural domains
+  - Protein folding, stability and design
+  - Structure prediction
+  - Sequence sites, features and motifs
+  - Metagenomics
   galaxy: ''
   homepage: http://colabfold.mmseqs.com
   id: colabfold_batch
@@ -3857,19 +3512,13 @@
     \ outputs the probabilities p (0 \u2264 p \u2264 1), which measure the likelihood\
     \ of protein coding."
   edam-operations:
-  - term: Regression analysis
-    url: http://edamontology.org/operation_3659
-  - term: Query and retrieval
-    url: http://edamontology.org/operation_0224
+  - Regression analysis
+  - Query and retrieval
   edam-topics:
-  - term: Functional, regulatory and non-coding RNA
-    url: http://edamontology.org/topic_0659
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
+  - Functional, regulatory and non-coding RNA
+  - Gene transcripts
+  - RNA-Seq
+  - Transcription factors and regulatory sites
   galaxy:
   - description: 'CPAT: coding potential assessment'
     title: CPAT 3.0.5+galaxy0
@@ -3896,8 +3545,7 @@
     individual variation.
   edam-operations: ''
   edam-topics:
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
+  - Genetic variation
   galaxy: ''
   homepage: https://github.com/crisflash/crisflash
   id: crisflash
@@ -3968,8 +3616,7 @@
     \ pooling, normalization, and activation layers."
   edam-operations: ''
   edam-topics:
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
+  - Machine learning
   galaxy: ''
   homepage: https://developer.nvidia.com/cudnn
   id: cudnn
@@ -3994,17 +3641,12 @@
     parsimonious set of transcripts. Cufflinks then estimates the relative abundances
     of these transcripts based on how many reads support each one.
   edam-operations:
-  - term: RNA-seq time series data analysis
-    url: http://edamontology.org/operation_3565
-  - term: Transcriptome assembly
-    url: http://edamontology.org/operation_3258
+  - RNA-seq time series data analysis
+  - Transcriptome assembly
   edam-topics:
-  - term: RNA splicing
-    url: http://edamontology.org/topic_3320
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - RNA splicing
+  - Transcriptomics
+  - RNA-Seq
   galaxy:
   - description: 'Cuffcompare: compare assembled transcripts to a reference annotation
       and track Cufflinks transcripts across multiple experiments'
@@ -4053,13 +3695,10 @@
     of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting
     functions for commonly used visualizations.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
-  - term: Sequence visualisation
-    url: http://edamontology.org/operation_0564
+  - Sequence analysis
+  - Sequence visualisation
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Sequencing
   galaxy:
   - description: 'cummeRbund: visualize Cuffdiff output'
     title: cummeRbund 2.16.0+galaxy1
@@ -4084,17 +3723,12 @@
   description: Generate customized protein sequence database from RNA-Seq data for
     proteomics search.
   edam-operations:
-  - term: Generation
-    url: http://edamontology.org/operation_3429
-  - term: Sequence annotation
-    url: http://edamontology.org/operation_0361
+  - Generation
+  - Sequence annotation
   edam-topics:
-  - term: Data integration and warehousing
-    url: http://edamontology.org/topic_3366
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Data integration and warehousing
+  - RNA-Seq
+  - Sequencing
   galaxy:
   - description: 'CustomProDB: Generate protein FASTAs from exosome or transcriptome
       data'
@@ -4122,19 +3756,13 @@
   description: Find and remove adapter sequences, primers, poly-A tails and other
     types of unwanted sequence from your high-throughput sequencing reads.
   edam-operations:
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Primer removal
-    url: http://edamontology.org/operation_3237
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
+  - Sequence trimming
+  - Primer removal
+  - Read pre-processing
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Probes and primers
-    url: http://edamontology.org/topic_0632
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Genomics
+  - Probes and primers
+  - Sequencing
   galaxy:
   - description: 'Cutadapt: Remove adapter sequences from FASTQ/FASTA'
     title: Cutadapt 4.8+galaxy1
@@ -4170,19 +3798,13 @@
     yields on real datasets. Further, its speed and scalability are outstanding and
     promising to large-scale data analysis
   edam-operations:
-  - term: Split read mapping
-    url: http://edamontology.org/operation_3199
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Structural variation detection
-    url: http://edamontology.org/operation_3228
+  - Split read mapping
+  - Genotyping
+  - Structural variation detection
   edam-topics:
-  - term: DNA structural variation
-    url: http://edamontology.org/topic_3175
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - DNA structural variation
+  - Sequencing
+  - Computer science
   galaxy:
   - description: 'cuteSV: detects long-read-based SVs'
     title: cuteSV 1.0.8+galaxy0
@@ -4213,19 +3835,13 @@
     classification is available via a native implementation of the RDP naive Bayesian
     classifier.
   edam-operations:
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: DNA barcoding
-    url: http://edamontology.org/operation_3200
+  - Variant calling
+  - DNA barcoding
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Microbial ecology
-    url: http://edamontology.org/topic_3697
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Sequencing
+  - Genetic variation
+  - Microbial ecology
+  - Metagenomics
   galaxy:
   - description: 'dada2: sequence counts: '
     title: 'dada2: sequence counts 1.30.0+galaxy0'
@@ -4400,15 +4016,11 @@
   description: User-friendly tools for the normalization and visualization of deep-sequencing
     data.
   edam-operations:
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Standardisation and normalisation
+  - Visualisation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
+  - Genomics
+  - ChIP-seq
   galaxy:
   - description: 'bamCompare: normalizes and compares two BAM or CRAM files to obtain
       the ratio, log2ratio or difference between them'
@@ -4498,21 +4110,14 @@
     trees and character matrices, and supports the reading and writing of phylogenetic
     data in a range of formats.
   edam-operations:
-  - term: Phylogenetic inference
-    url: http://edamontology.org/operation_0323
-  - term: Phylogenetic tree distances calculation
-    url: http://edamontology.org/operation_0557
-  - term: Phylogenetic tree editing
-    url: http://edamontology.org/operation_0326
-  - term: Phylogenetic tree topology analysis
-    url: http://edamontology.org/operation_0551
-  - term: Phylogenetic tree bootstrapping
-    url: http://edamontology.org/operation_0552
-  edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
+  - Phylogenetic inference
+  - Phylogenetic tree distances calculation
+  - Phylogenetic tree editing
+  - Phylogenetic tree topology analysis
+  - Phylogenetic tree bootstrapping
+  edam-topics:
+  - Phylogenetics
+  - Phylogenomics
   galaxy: ''
   homepage: https://dendropy.org/
   id: dendropy
@@ -4556,13 +4161,10 @@
     data from high-throughput sequencing assays and test for differential expression
     based on a model using the negative binomial distribution.
   edam-operations:
-  - term: Differential gene expression analysis
-    url: http://edamontology.org/operation_3223
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
+  - Differential gene expression analysis
+  - RNA-Seq analysis
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - RNA-Seq
   galaxy:
   - description: 'DESeq2: Determines differentially expressed features from count
       tables'
@@ -4592,13 +4194,10 @@
     biological replicates and generalized linear models for testing. The package also
     provides functions for the visualization and exploration of the results.
   edam-operations:
-  - term: Enrichment analysis
-    url: http://edamontology.org/operation_3501
-  - term: Exonic splicing enhancer prediction
-    url: http://edamontology.org/operation_0446
+  - Enrichment analysis
+  - Exonic splicing enhancer prediction
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - RNA-Seq
   galaxy:
   - description: 'plotDEXSeq: Visualization of the per gene DEXSeq results'
     title: plotDEXSeq 1.48.0+galaxy0
@@ -4631,23 +4230,15 @@
     sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome
     annotations.
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  - term: Sequence visualisation
-    url: http://edamontology.org/operation_0564
-  - term: Pairwise sequence alignment
-    url: http://edamontology.org/operation_0491
-  edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
-  - term: Mobile genetic elements
-    url: http://edamontology.org/topic_0798
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Plant biology
-    url: http://edamontology.org/topic_0780
+  - Genome annotation
+  - Sequence visualisation
+  - Pairwise sequence alignment
+  edam-topics:
+  - DNA
+  - Phylogeny
+  - Mobile genetic elements
+  - Sequence assembly
+  - Plant biology
   galaxy: ''
   homepage: https://dfam.org
   id: dfam
@@ -4677,23 +4268,15 @@
     DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper
     for DiaNN.exe)'
   edam-operations:
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Spectral library search
-    url: http://edamontology.org/operation_3801
-  - term: Protein identification
-    url: http://edamontology.org/operation_3767
-  edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
+  - Quantification
+  - Spectral library search
+  - Protein identification
+  edam-topics:
+  - Proteomics
+  - Proteomics experiment
+  - Sequence analysis
+  - Machine learning
+  - Small molecules
   galaxy:
   - description: 'DIA-NN: is a software for DIA/SWATH data processing'
     title: DIA-NN 1.8.1+galaxy3
@@ -4721,19 +4304,13 @@
     DIA data, and also incorporates targeted extraction to reduce the number of cases
     of missing quantitation.
   edam-operations:
-  - term: Peak detection
-    url: http://edamontology.org/operation_3215
-  - term: Spectrum calculation
-    url: http://edamontology.org/operation_3860
-  - term: Retention time prediction
-    url: http://edamontology.org/operation_3633
-  - term: Mass spectra calibration
-    url: http://edamontology.org/operation_3627
+  - Peak detection
+  - Spectrum calculation
+  - Retention time prediction
+  - Mass spectra calibration
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
+  - Proteomics
+  - Proteomics experiment
   galaxy:
   - description: 'DIA_Umpire_SE: DIA signal extraction'
     title: DIA_Umpire_SE 2.1.3.0
@@ -4764,13 +4341,10 @@
     sequences including contigs and assemblies, providing a speedup of BLAST ranging
     up to x20,000.
   edam-operations:
-  - term: Sequence alignment analysis
-    url: http://edamontology.org/operation_0258
+  - Sequence alignment analysis
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Proteins
-    url: http://edamontology.org/topic_0078
+  - Sequence analysis
+  - Proteins
   galaxy:
   - description: 'Diamond: alignment tool for short sequences against a protein database'
     title: Diamond 2.0.15+galaxy0
@@ -4802,23 +4376,15 @@
   description: diaPASEF is an appproch for parallel accumulation-serial fragmentation
     combined with data-independent acquisition.
   edam-operations:
-  - term: Deisotoping
-    url: http://edamontology.org/operation_3629
-  - term: Ion counting
-    url: http://edamontology.org/operation_3704
-  - term: Protein identification
-    url: http://edamontology.org/operation_3767
-  edam-topics:
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
+  - Deisotoping
+  - Ion counting
+  - Protein identification
+  edam-topics:
+  - Proteomics experiment
+  - Proteomics
+  - Sequence analysis
+  - Sequencing
+  - Small molecules
   galaxy:
   - description: 'diapysef library generation: generates spectral library for DIA
       analysis'
@@ -4845,11 +4411,9 @@
     using affinity (quantitative) data. Also enables occupancy (overlap) analysis
     and plotting functions.
   edam-operations:
-  - term: Differential binding analysis
-    url: http://edamontology.org/operation_3677
+  - Differential binding analysis
   edam-topics:
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
+  - ChIP-seq
   galaxy:
   - description: 'DiffBind: differential binding analysis of ChIP-Seq peak data'
     title: DiffBind 2.10.0+galaxy1
@@ -4916,17 +4480,12 @@
     identification of cells from empty droplets, removal of barcode-swapped pseudo-cells,
     and downsampling of the count matrix.
   edam-operations:
-  - term: Loading
-    url: http://edamontology.org/operation_1812
+  - Loading
   edam-topics:
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - Gene expression
+  - RNA-seq
+  - Sequencing
+  - Transcriptomics
   galaxy:
   - description: 'DropletUtils: Utilities for handling droplet-based single-cell RNA-seq
       data'
@@ -4991,25 +4550,16 @@
   - '1.10'
   description: Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool.
   edam-operations:
-  - term: Imputation
-    url: http://edamontology.org/operation_3557
-  - term: Phasing
-    url: http://edamontology.org/operation_3454
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Genome indexing
-    url: http://edamontology.org/operation_3211
-  edam-topics:
-  - term: Genotype and phenotype
-    url: http://edamontology.org/topic_0625
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: GWAS study
-    url: http://edamontology.org/topic_3517
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Imputation
+  - Phasing
+  - Genotyping
+  - Genome indexing
+  edam-topics:
+  - Genotype and phenotype
+  - Sequencing
+  - GWAS study
+  - DNA
+  - Computer science
   galaxy: ''
   homepage: https://github.com/ikmb/eagleimp
   id: eagleimp
@@ -5032,11 +4582,9 @@
     you to manage (scientific) software on High Performance Computing (HPC) systems
     in an efficient way.
   edam-operations:
-  - term: Service management
-    url: http://edamontology.org/operation_3760
+  - Service management
   edam-topics:
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Computer science
   galaxy: ''
   homepage: https://github.com/easybuilders/easybuild
   id: easybuild
@@ -5080,15 +4628,11 @@
     it be applied to differential signal analysis of other types of genomic data that
     produce counts, including ChIP-seq, SAGE and CAGE.
   edam-operations:
-  - term: Differential gene expression analysis
-    url: http://edamontology.org/operation_3223
+  - Differential gene expression analysis
   edam-topics:
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
+  - Genetics
+  - RNA-Seq
+  - ChIP-seq
   galaxy:
   - description: 'edgeR: Perform differential expression of count data'
     title: edgeR 3.36.0+galaxy4
@@ -5123,15 +4667,11 @@
     it be applied to differential signal analysis of other types of genomic data that
     produce counts, including ChIP-seq, SAGE and CAGE.
   edam-operations:
-  - term: Differential gene expression analysis
-    url: http://edamontology.org/operation_3223
+  - Differential gene expression analysis
   edam-topics:
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
+  - Genetics
+  - RNA-Seq
+  - ChIP-seq
   galaxy:
   - description: 'edgeR-repenrich: Determines differentially expressed features from
       RepEnrich counts'
@@ -5166,11 +4706,9 @@
     It supports searching by indexed terms, looking up precomputed neighbors or links,
     filtering results by date or category, and downloading record summaries or reports.
   edam-operations:
-  - term: Information retrieval
-    url: http://edamontology.org/operation_3908
+  - Information retrieval
   edam-topics:
-  - term: Data integration and warehousing
-    url: http://edamontology.org/topic_3366
+  - Data integration and warehousing
   galaxy: ''
   homepage: https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect
   id: edirect
@@ -5196,13 +4734,10 @@
     than traditional homology searches, as it avoids transferring annotations from
     close paralogs.'
   edam-operations:
-  - term: Database search
-    url: http://edamontology.org/operation_2421
+  - Database search
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Metagenomics
+  - Genomics
   galaxy:
   - description: 'eggNOG Mapper: functional sequence annotation by orthology'
     title: eggNOG Mapper 2.1.8+galaxy4
@@ -5239,11 +4774,9 @@
   description: This package implements the Ensemble of Gene Set Enrichment Analyses
     method for gene set testing.
   edam-operations:
-  - term: Gene set testing
-    url: http://edamontology.org/operation_3224
+  - Gene set testing
   edam-topics:
-  - term: Systems biology
-    url: http://edamontology.org/topic_2259
+  - Systems biology
   galaxy:
   - description: 'EGSEA: easy and efficient ensemble gene set testing'
     title: EGSEA 1.20.0
@@ -5285,15 +4818,11 @@
     elastix is accompanied by SimpleElastix , making it available in languages like
     C++, Python, Java, R, Ruby, C# and Lua.'
   edam-operations:
-  - term: Image analysis
-    url: http://edamontology.org/operation_3443
+  - Image analysis
   edam-topics:
-  - term: Medical imaging
-    url: http://edamontology.org/topic_3384
-  - term: Oncology
-    url: http://edamontology.org/topic_2640
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
+  - Medical imaging
+  - Oncology
+  - Model organisms
   galaxy: ''
   homepage: http://elastix.isi.uu.nl
   id: elastix
@@ -5323,23 +4852,15 @@
   description: Diverse suite of tools for sequence analysis; many programs analagous
     to GCG; context-sensitive help for each tool.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
-  - term: Local alignment
-    url: http://edamontology.org/operation_0495
-  - term: Sequence alignment analysis
-    url: http://edamontology.org/operation_0258
-  - term: Global alignment
-    url: http://edamontology.org/operation_0496
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  edam-topics:
-  - term: Molecular biology
-    url: http://edamontology.org/topic_3047
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Biology
-    url: http://edamontology.org/topic_3070
+  - Sequence analysis
+  - Local alignment
+  - Sequence alignment analysis
+  - Global alignment
+  - Sequence alignment
+  edam-topics:
+  - Molecular biology
+  - Sequence analysis
+  - Biology
   galaxy:
   - description: 'dreg: Regular expression search of a nucleotide sequence'
     title: dreg 5.0.0+galaxy1
@@ -5686,23 +5207,15 @@
     both as the database of record for the output of the world's sequencing activity
     and as a platform for the management, sharing and publication of sequence data.
   edam-operations:
-  - term: Sequence similarity search
-    url: http://edamontology.org/operation_0346
-  - term: Deposition
-    url: http://edamontology.org/operation_3431
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Data retrieval
-    url: http://edamontology.org/operation_2422
-  edam-topics:
-  - term: Data submission, annotation and curation
-    url: http://edamontology.org/topic_0219
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: Nucleic acid sites, features and motifs
-    url: http://edamontology.org/topic_3511
+  - Sequence similarity search
+  - Deposition
+  - Sequence assembly
+  - Data retrieval
+  edam-topics:
+  - Data submission, annotation and curation
+  - Transcription factors and regulatory sites
+  - Gene transcripts
+  - Nucleic acid sites, features and motifs
   galaxy:
   - description: 'ENA Upload tool: Submission of (meta)data to the European Nucleotide
       Archive (ENA)'
@@ -5734,13 +5247,10 @@
     for DIA data analysis and can search for peptides using either DDA-based spectrum
     libraries or DIA-based chromatogram libraries.
   edam-operations:
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Formatting
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
+  - Proteomics
+  - Proteomics experiment
   galaxy:
   - description: 'SearchToLib: Build a Chromatogram Library from Data-Independent
       Acquisition (DIA) MS/MS Data'
@@ -5858,25 +5368,16 @@
     and Trypanosoma. The database portal offers an entry point to all these resources,
     and the opportunity to leverage orthology for searches across genera.
   edam-operations:
-  - term: Database search
-    url: http://edamontology.org/operation_2421
-  - term: Deposition
-    url: http://edamontology.org/operation_3431
-  - term: Generation
-    url: http://edamontology.org/operation_3429
-  - term: Query and retrieval
-    url: http://edamontology.org/operation_0224
-  - term: Data retrieval
-    url: http://edamontology.org/operation_2422
-  edam-topics:
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: Zoology
-    url: http://edamontology.org/topic_3500
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
+  - Database search
+  - Deposition
+  - Generation
+  - Query and retrieval
+  - Data retrieval
+  edam-topics:
+  - Model organisms
+  - Model organisms
+  - Zoology
+  - Gene transcripts
   galaxy:
   - description: 'EuPathDB: server'
     title: EuPathDB 1.0.0
@@ -5900,15 +5401,11 @@
   description: ExaBayes is a software package for Bayesian phylogenetic tree inference.
     It is particularly suitable for large-scale analyses on computer clusters.
   edam-operations:
-  - term: Phylogenetic inference
-    url: http://edamontology.org/operation_0323
-  - term: Phylogenetic tree editing
-    url: http://edamontology.org/operation_0326
-  - term: Phylogenetic tree topology analysis
-    url: http://edamontology.org/operation_0551
+  - Phylogenetic inference
+  - Phylogenetic tree editing
+  - Phylogenetic tree topology analysis
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
+  - Phylogenetics
   galaxy: ''
   homepage: https://github.com/aberer/exabayes
   id: exabayes
@@ -5927,15 +5424,11 @@
   bunya: ''
   description: Tool for phylogenomic analyses on supercomputers.
   edam-operations:
-  - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
-    url: http://edamontology.org/operation_0547
+  - Phylogenetic tree generation (maximum likelihood and Bayesian methods)
   edam-topics:
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
-  - term: Literature and language
-    url: http://edamontology.org/topic_3068
+  - Phylogeny
+  - Phylogenomics
+  - Literature and language
   galaxy: ''
   homepage: https://github.com/stamatak/ExaML
   id: examl
@@ -5958,19 +5451,13 @@
   description: A tool for pairwise sequence alignment. It enables alignment for DNA-DNA
     and DNA-protein pairs and also gapped and ungapped alignment.
   edam-operations:
-  - term: Pairwise sequence alignment
-    url: http://edamontology.org/operation_0491
-  - term: Protein threading
-    url: http://edamontology.org/operation_0302
-  - term: Genome alignment
-    url: http://edamontology.org/operation_3182
+  - Pairwise sequence alignment
+  - Protein threading
+  - Genome alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
+  - Sequence analysis
+  - Sequence sites, features and motifs
+  - Molecular interactions, pathways and networks
   galaxy:
   - description: 'Exonerate: pairwise sequence comparison'
     title: Exonerate 2.4.0+galaxy2
@@ -6018,15 +5505,11 @@
     and tree file for GraPhlAn. In particular, the annotation file tries to highlight
     specific sub-trees deriving automatically from input file what nodes are important.
   edam-operations:
-  - term: Conversion
-    url: http://edamontology.org/operation_3434
+  - Conversion
   edam-topics:
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
-  - term: Biomarkers
-    url: http://edamontology.org/topic_3360
+  - Taxonomy
+  - Metabolomics
+  - Biomarkers
   galaxy:
   - description: 'Export to GraPhlAn: '
     title: Export to GraPhlAn 0.20+galaxy0
@@ -6055,17 +5538,12 @@
     data. It can be used to resolve ambiguous mappings in other high-throughput sequencing
     based applications.
   edam-operations:
-  - term: Imputation
-    url: http://edamontology.org/operation_3557
+  - Imputation
   edam-topics:
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
+  - Gene expression
+  - Metagenomics
+  - RNA-seq
+  - ChIP-seq
   galaxy:
   - description: 'eXpress: Quantify the abundances of a set of target sequences from
       sampled subsequences'
@@ -6112,11 +5590,9 @@
   - 0.0.8--hdfd78af_1
   description: Experimental PacBio diploid assembler.
   edam-operations:
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
+  - Sequence assembly
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy: ''
   homepage: https://github.com/pratas/falcon
   id: pb-assembly
@@ -6136,15 +5612,11 @@
   bunya: ''
   description: Add length of sequence to fasta header.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: Nucleic acids
-    url: http://edamontology.org/topic_0077
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Nucleic acids
+  - Sequence analysis
+  - Data management
   galaxy:
   - description: 'Compute sequence length: '
     title: Compute sequence length 1.0.3
@@ -6299,15 +5771,11 @@
     of orthologous gene pairs shared between two microbial genomes. FastANI supports
     pairwise comparison of both complete and draft genome assemblies.
   edam-operations:
-  - term: Genome alignment
-    url: http://edamontology.org/operation_3182
-  - term: Sequence similarity search
-    url: http://edamontology.org/operation_0346
+  - Genome alignment
+  - Sequence similarity search
   edam-topics:
-  - term: Microbiology
-    url: http://edamontology.org/topic_3301
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
+  - Microbiology
+  - Genetic variation
   galaxy: ''
   homepage: https://github.com/ParBLiSS/FastANI
   id: fastani
@@ -6327,11 +5795,9 @@
   description: Read huge FastQ and FastA files (both normal and gzipped) an demanipulate
     them.
   edam-operations:
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Formatting
   edam-topics:
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Data management
   galaxy: ''
   homepage: https://github.com/fstrozzi/Fastool
   id: fastool
@@ -6352,15 +5818,11 @@
     files. This tool is developed in C++ with multithreading supported to afford high
     performance.
   edam-operations:
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Sequence contamination filtering
-    url: http://edamontology.org/operation_3187
+  - Sequencing quality control
+  - Sequence contamination filtering
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Probes and primers
-    url: http://edamontology.org/topic_0632
+  - Sequence analysis
+  - Probes and primers
   galaxy:
   - description: 'fastp: fast all-in-one preprocessing for FASTQ files'
     title: fastp 0.23.4+galaxy0
@@ -6391,19 +5853,13 @@
     into a larger analysis pipeline for the systematic processing of large numbers
     of files.
   edam-operations:
-  - term: Sequence composition calculation
-    url: http://edamontology.org/operation_0236
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
+  - Sequence composition calculation
+  - Sequencing quality control
+  - Statistical calculation
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Data quality management
-    url: http://edamontology.org/topic_3572
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequencing
+  - Data quality management
+  - Sequence analysis
   galaxy:
   - description: 'FastQC: Read Quality reports'
     title: FastQC 0.74+galaxy0
@@ -6452,15 +5908,11 @@
   description: Infers approximately-maximum-likelihood phylogenetic trees from alignments
     of nucleotide or protein sequences.
   edam-operations:
-  - term: Phylogenetic tree generation (from molecular sequences)
-    url: http://edamontology.org/operation_0540
-  - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
-    url: http://edamontology.org/operation_0547
+  - Phylogenetic tree generation (from molecular sequences)
+  - Phylogenetic tree generation (maximum likelihood and Bayesian methods)
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Phylogenetics
+  - Sequence analysis
   galaxy:
   - description: 'FASTTREE: build maximum-likelihood phylogenetic trees'
     title: FASTTREE 2.1.10+galaxy1
@@ -6487,13 +5939,10 @@
   description: Collection of command line tools for Short-Reads FASTA/FASTQ files
     preprocessing.
   edam-operations:
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
-  - term: Sequence editing
-    url: http://edamontology.org/operation_0231
+  - Read pre-processing
+  - Sequence editing
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'Remove sequencing artifacts: '
     title: Remove sequencing artifacts 1.0.1+galaxy2
@@ -6541,13 +5990,10 @@
   description: Collection of command line tools for Short-Reads FASTA/FASTQ files
     preprocessing.
   edam-operations:
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
-  - term: Sequence editing
-    url: http://edamontology.org/operation_0231
+  - Read pre-processing
+  - Sequence editing
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'Length Distribution: chart'
     title: Length Distribution 1.0.1+galaxy2
@@ -6602,11 +6048,9 @@
   description: HMM-based gene structure prediction (multiple genes, both chains);
     Program for predicting multiple genes in genomic DNA sequences.
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
+  - Gene prediction
   edam-topics:
-  - term: Gene structure
-    url: http://edamontology.org/topic_0114
+  - Gene structure
   galaxy:
   - description: 'FGENESH get protein: sequences using rensn3 files'
     title: FGENESH get protein 1.0.0+galaxy0
@@ -6632,11 +6076,9 @@
     p-values, which allows to use accurate stantard approaches to multiple hypothesis
     correction.
   edam-operations:
-  - term: Gene-set enrichment analysis
-    url: http://edamontology.org/operation_2436
+  - Gene-set enrichment analysis
   edam-topics:
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
+  - Genetics
   galaxy:
   - description: 'fgsea: - fast preranked gene set enrichment analysis'
     title: fgsea 1.8.0+galaxy1
@@ -6683,10 +6125,8 @@
     (longer is better) and read identity (higher is better) when choosing which reads
     pass the filter.
   edam-operations:
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
+  - Filtering
+  - Sequencing quality control
   edam-topics: ''
   galaxy:
   - description: 'filtlong: Filtering long reads by quality'
@@ -6709,13 +6149,10 @@
   description: FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry
     proteomics.
   edam-operations:
-  - term: Label-free quantification
-    url: http://edamontology.org/operation_3634
+  - Label-free quantification
   edam-topics:
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
+  - Proteomics experiment
+  - Proteomics
   galaxy:
   - description: 'FlashLFQ: ultrafast label-free quantification for mass-spectrometry
       proteomics'
@@ -6763,23 +6200,15 @@
     assemblies. The package represents a complete pipeline: it takes raw PB / ONT
     reads as input and outputs polished contigs.'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Mapping assembly
-    url: http://edamontology.org/operation_0523
-  - term: Cross-assembly
-    url: http://edamontology.org/operation_3730
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genome assembly
+  - De-novo assembly
+  - Mapping assembly
+  - Cross-assembly
+  edam-topics:
+  - Sequence assembly
+  - Metagenomics
+  - Whole genome sequencing
+  - Genomics
   galaxy:
   - description: 'Flye: de novo assembler for single molecule sequencing reads'
     title: Flye 2.9.3+galaxy0
@@ -6833,11 +6262,9 @@
     sets. It reaches sensitivities similar to state-of-the-art structural aligners
     while being at least 20,000 times faster.
   edam-operations:
-  - term: Structure alignment
-    url: http://edamontology.org/operation_0295
+  - Structure alignment
   edam-topics:
-  - term: Proteins
-    url: http://edamontology.org/topic_0078
+  - Proteins
   galaxy: ''
   homepage: https://foldseek.com
   id: foldseek
@@ -6863,11 +6290,9 @@
     insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined
     analysis of homologous structures (hpocket).
   edam-operations:
-  - term: Molecular surface analysis
-    url: http://edamontology.org/operation_3351
+  - Molecular surface analysis
   edam-topics:
-  - term: Protein structural motifs and surfaces
-    url: http://edamontology.org/topic_0166
+  - Protein structural motifs and surfaces
   galaxy:
   - description: 'dpocket: to calculate descriptors for protein pockets'
     title: dpocket 4.0.0+galaxy0
@@ -6895,13 +6320,10 @@
   bunya: ''
   description: Application for finding (fragmented) genes in short reads
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
+  - Gene prediction
   edam-topics:
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Genetics
+  - Sequence analysis
   galaxy:
   - description: 'FragGeneScan: for finding (fragmented) genes in short reads'
     title: FragGeneScan 1.30.0
@@ -6930,17 +6352,12 @@
     (composite insertion and substitution events) smaller than the length of a short-read
     sequencing alignment.
   edam-operations:
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
+  - Variant calling
+  - Statistical calculation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Rare diseases
-    url: http://edamontology.org/topic_3325
+  - Genomics
+  - Genetic variation
+  - Rare diseases
   galaxy:
   - description: 'BamLeftAlign: indels in BAM datasets'
     title: BamLeftAlign 1.3.6
@@ -6984,11 +6401,9 @@
   description: funannotate is a pipeline for genome annotation (built specifically
     for fungi, but will also work with higher eukaryotes).
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Genome annotation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy:
   - description: 'Funannotate functional: annotation'
     title: Funannotate functional 1.8.15+galaxy5
@@ -7021,13 +6436,10 @@
   bunya: ''
   description: Gene Annotation EVAluation.
   edam-operations:
-  - term: Sequence annotation
-    url: http://edamontology.org/operation_0361
+  - Sequence annotation
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Gene structure
-    url: http://edamontology.org/topic_0114
+  - Sequence analysis
+  - Gene structure
   galaxy:
   - description: 'AEGeAn CanonGFF3: pre-process GFF3 files, removing all features
       not directly related to protein-coding genes'
@@ -7140,190 +6552,190 @@
   - description: 'AXT to LAV: Converts an AXT formatted file to LAV format'
     title: AXT to LAV 1.0.0
     url: https://usegalaxy.org.au/root?tool_id=axt_to_lav_1
-  - description: 'Convert SMILES to MOL: '
-    title: Convert SMILES to MOL 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL
-  - description: 'Convert compressed file to uncompressed.: '
-    title: Convert compressed file to uncompressed. 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed
-  - description: 'Convert tabular to dbnsfp: '
-    title: Convert tabular to dbnsfp 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp
-  - description: 'Convert Genomic Intervals To Strict BED12: '
-    title: Convert Genomic Intervals To Strict BED12 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0
-  - description: 'Convert uncompressed file to compressed: '
-    title: Convert uncompressed file to compressed 1.16+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz
-  - description: 'Convert InChI to MOL: '
-    title: Convert InChI to MOL 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol
-  - description: 'OpenBabel converter for molecular formats: '
-    title: OpenBabel converter for molecular formats 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules
-  - description: 'Convert GFF to BED: '
-    title: Convert GFF to BED 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0
-  - description: 'Convert BAM to BigWig: '
-    title: Convert BAM to BigWig 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0
-  - description: 'Convert BAM to queryname-sorted BAM: '
-    title: Convert BAM to queryname-sorted BAM 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam
+  - description: 'Convert FASTA to Tabular: '
+    title: Convert FASTA to Tabular 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular
+  - description: 'Convert GFF to Interval Index: '
+    title: Convert GFF to Interval Index 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0
+  - description: 'Convert Biom datasets: '
+    title: Convert Biom datasets 2.1.5
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom
   - description: 'Convert FASTQ files to seek locations: '
     title: Convert FASTQ files to seek locations 1.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0
-  - description: 'Convert MAF to Genomic Intervals: '
-    title: Convert MAF to Genomic Intervals 1.0.3
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0
-  - description: 'Convert Wiggle to Interval: '
-    title: Convert Wiggle to Interval 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0
+  - description: 'OpenBabel converter for molecular formats: '
+    title: OpenBabel converter for molecular formats 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules
+  - description: 'Convert uncompressed file to compressed: '
+    title: Convert uncompressed file to compressed 1.16+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz
   - description: 'Convert Interval to tabix: '
     title: Convert Interval to tabix 1.0.2
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0
-  - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence
-      taxonomy file to a 2 column mothur taxonomy_outline format'
-    title: Convert Ref taxonomy to Seq Taxonomy 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony
-  - description: 'Convert BED to Feature Location Index: '
-    title: Convert BED to Feature Location Index 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0
-  - description: 'Convert XTC, DCD, and TRR: '
-    title: Convert XTC, DCD, and TRR 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert
-  - description: 'Convert Genomic Intervals To Strict BED6: '
-    title: Convert Genomic Intervals To Strict BED6 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0
-  - description: 'Convert plink pbed to linkage lped: '
-    title: Convert plink pbed to linkage lped 0.02
-    url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert
-  - description: 'Convert tar to directory: '
-    title: Convert tar to directory 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory
-  - description: 'Convert tabular to CSV: '
-    title: Convert tabular to CSV 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv
+  - description: 'Convert PDB to GRO: '
+    title: Convert PDB to GRO 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0
   - description: 'Convert Interval to BGZIP: '
     title: Convert Interval to BGZIP 1.0.3
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0
-  - description: 'Convert FASTA to len file: '
-    title: Convert FASTA to len file 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len
+  - description: 'Convert Bam to Bai: '
+    title: Convert Bam to Bai 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0
+  - description: 'Convert lped to fped: '
+    title: Convert lped to fped 0.02
+    url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert
+  - description: 'Convert CRAM to BAM: '
+    title: Convert CRAM to BAM 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0
+  - description: 'Convert tar to directory: '
+    title: Convert tar to directory 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory
   - description: 'Convert GFF to Feature Location Index: '
     title: Convert GFF to Feature Location Index 1.0.0
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0
-  - description: 'Convert GFF to Interval Index: '
-    title: Convert GFF to Interval Index 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0
   - description: 'Convert FASTA to fai file: '
     title: Convert FASTA to fai file 1.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai
+  - description: 'Convert tabular to dbnsfp: '
+    title: Convert tabular to dbnsfp 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp
+  - description: 'Convert Len file to Linecount: '
+    title: Convert Len file to Linecount 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount
+  - description: 'Convert BED, GFF, or VCF to BigWig: '
+    title: Convert BED, GFF, or VCF to BigWig 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0
+  - description: 'Convert XTC, DCD, and TRR: '
+    title: Convert XTC, DCD, and TRR 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert
+  - description: 'Convert compressed file to uncompressed.: '
+    title: Convert compressed file to uncompressed. 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed
+  - description: 'Convert SAM to BAM without sorting: '
+    title: Convert SAM to BAM without sorting 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam
   - description: 'Convert compressed file to uncompressed.: '
     title: Convert compressed file to uncompressed. 1.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed
+  - description: 'Convert MAF to Fasta: '
+    title: Convert MAF to Fasta 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0
+  - description: 'Convert tabular to CSV: '
+    title: Convert tabular to CSV 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv
+  - description: 'Convert lped to plink pbed: '
+    title: Convert lped to plink pbed 0.02
+    url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert
+  - description: 'Convert MOL2 to MOL: '
+    title: Convert MOL2 to MOL 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol
+  - description: 'Convert Picard Interval List to BED6: converter'
+    title: Convert Picard Interval List to BED6 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6
+  - description: 'Convert BAM to BigWig: '
+    title: Convert BAM to BigWig 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0
+  - description: 'Convert BED to GFF: '
+    title: Convert BED to GFF 2.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0
   - description: 'Convert CSV to tabular: '
     title: Convert CSV to tabular 1.0.0
     url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular
-  - description: 'Convert neostore.zip files to neostore: '
-    title: Convert neostore.zip files to neostore 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore
-  - description: 'Convert FASTA to 2bit: '
-    title: Convert FASTA to 2bit 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit
-  - description: 'Convert BGZ VCF to tabix: '
-    title: Convert BGZ VCF to tabix 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0
-  - description: 'Convert Biom datasets: '
-    title: Convert Biom datasets 2.1.5
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom
-  - description: 'Convert FASTA to Bowtie base space Index: '
-    title: Convert FASTA to Bowtie base space Index 1.3.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index
+  - description: 'Convert Parquet to csv: '
+    title: Convert Parquet to csv 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv
+  - description: 'Convert GRO to PDB: '
+    title: Convert GRO to PDB 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0
   - description: 'Convert compressed and uncompressed BCF files: '
     title: Convert compressed and uncompressed BCF files 0.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf
-  - description: 'Convert Bam to Bai: '
-    title: Convert Bam to Bai 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0
-  - description: 'Convert BED, GFF, or VCF to BigWig: '
-    title: Convert BED, GFF, or VCF to BigWig 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0
+  - description: 'Convert BAM to queryname-sorted BAM: '
+    title: Convert BAM to queryname-sorted BAM 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam
+  - description: 'Convert BAM to coordinate-sorted BAM: '
+    title: Convert BAM to coordinate-sorted BAM 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam
+  - description: 'Convert Genomic Intervals To BED: '
+    title: Convert Genomic Intervals To BED 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0
   - description: 'SMILES to SMILES: '
     title: SMILES to SMILES 2.4.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles
-  - description: 'Convert PDB to GRO: '
-    title: Convert PDB to GRO 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0
+  - description: 'Convert CML to SMILES: '
+    title: Convert CML to SMILES 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles
+  - description: 'Convert plink pbed to linkage lped: '
+    title: Convert plink pbed to linkage lped 0.02
+    url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert
+  - description: 'Convert plink pbed to ld reduced format: '
+    title: Convert plink pbed to ld reduced format 0.02
+    url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert
+  - description: 'Convert Wiggle to Interval: '
+    title: Convert Wiggle to Interval 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0
   - description: 'Convert FASTA to Bowtie color space Index: '
     title: Convert FASTA to Bowtie color space Index 1.2.3
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index
-  - description: 'Convert BED to GFF: '
-    title: Convert BED to GFF 2.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0
-  - description: 'Convert Len file to Linecount: '
-    title: Convert Len file to Linecount 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount
-  - description: 'Convert Picard Interval List to BED6: converter'
-    title: Convert Picard Interval List to BED6 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6
-  - description: 'Convert FASTA to Tabular: '
-    title: Convert FASTA to Tabular 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular
-  - description: 'Convert MAF to Fasta: '
-    title: Convert MAF to Fasta 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0
-  - description: 'Convert BedGraph to BigWig: '
-    title: Convert BedGraph to BigWig 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig
-  - description: 'Convert Parquet to csv: '
-    title: Convert Parquet to csv 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv
-  - description: 'Convert SAM to BAM without sorting: '
-    title: Convert SAM to BAM without sorting 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam
-  - description: 'Convert BigWig to Wiggle: Convert bigWig to wig'
-    title: Convert BigWig to Wiggle 377+galaxy0
-    url: https://usegalaxy.org.au/root?tool_id=bigwigtowig
-  - description: 'Convert Genomic Intervals To BED: '
-    title: Convert Genomic Intervals To BED 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0
+  - description: 'Convert InChI to MOL: '
+    title: Convert InChI to MOL 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol
+  - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence
+      taxonomy file to a 2 column mothur taxonomy_outline format'
+    title: Convert Ref taxonomy to Seq Taxonomy 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony
+  - description: 'Convert MAF to Genomic Intervals: '
+    title: Convert MAF to Genomic Intervals 1.0.3
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0
+  - description: 'Convert FASTA to Bowtie base space Index: '
+    title: Convert FASTA to Bowtie base space Index 1.3.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index
+  - description: 'Convert Genomic Intervals To Strict BED: '
+    title: Convert Genomic Intervals To Strict BED 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0
+  - description: 'Convert Genomic Intervals To Strict BED6: '
+    title: Convert Genomic Intervals To Strict BED6 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0
+  - description: 'Convert FASTA to 2bit: '
+    title: Convert FASTA to 2bit 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit
+  - description: 'Convert GFF to BED: '
+    title: Convert GFF to BED 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0
+  - description: 'Convert BGZ VCF to tabix: '
+    title: Convert BGZ VCF to tabix 1.0.2
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0
+  - description: 'Convert neostore.zip files to neostore: '
+    title: Convert neostore.zip files to neostore 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore
+  - description: 'Convert SMILES to MOL: '
+    title: Convert SMILES to MOL 2.4.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL
   - description: 'Convert SAM to BigWig: '
     title: Convert SAM to BigWig 1.0.3
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0
-  - description: 'Convert plink pbed to ld reduced format: '
-    title: Convert plink pbed to ld reduced format 0.02
-    url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert
-  - description: 'Convert lped to fped: '
-    title: Convert lped to fped 0.02
-    url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert
-  - description: 'Convert MOL2 to MOL: '
-    title: Convert MOL2 to MOL 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol
-  - description: 'Convert lped to plink pbed: '
-    title: Convert lped to plink pbed 0.02
-    url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert
-  - description: 'Convert Genomic Intervals To Coverage: '
-    title: Convert Genomic Intervals To Coverage 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0
-  - description: 'Convert BAM to coordinate-sorted BAM: '
-    title: Convert BAM to coordinate-sorted BAM 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam
-  - description: 'Convert GRO to PDB: '
-    title: Convert GRO to PDB 1.0.0
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0
   - description: 'Convert Wiggle to BigWig: '
     title: Convert Wiggle to BigWig 1.0.1
     url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig
-  - description: 'Convert CRAM to BAM: '
-    title: Convert CRAM to BAM 1.0.2
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0
-  - description: 'Convert Genomic Intervals To Strict BED: '
-    title: Convert Genomic Intervals To Strict BED 1.0.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0
-  - description: 'Convert CML to SMILES: '
-    title: Convert CML to SMILES 2.4.1
-    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles
+  - description: 'Convert Genomic Intervals To Strict BED12: '
+    title: Convert Genomic Intervals To Strict BED12 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0
+  - description: 'Convert Genomic Intervals To Coverage: '
+    title: Convert Genomic Intervals To Coverage 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0
+  - description: 'Convert FASTA to len file: '
+    title: Convert FASTA to len file 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len
+  - description: 'Convert BedGraph to BigWig: '
+    title: Convert BedGraph to BigWig 1.0.1
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig
+  - description: 'Convert BED to Feature Location Index: '
+    title: Convert BED to Feature Location Index 1.0.0
+    url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0
+  - description: 'Convert BigWig to Wiggle: Convert bigWig to wig'
+    title: Convert BigWig to Wiggle 377+galaxy0
+    url: https://usegalaxy.org.au/root?tool_id=bigwigtowig
   homepage: ''
   id: Galaxy CONVERTER
   license: ''
@@ -7668,23 +7080,15 @@
     \ number and somatic analyses and offers pipeline scripts for workflows.  \n\n\
     Version 4 (GATK4) is open-source at https://github.com/broadinstitute/gatk."
   edam-operations:
-  - term: Polymorphism detection
-    url: http://edamontology.org/operation_3202
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
-  edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - Polymorphism detection
+  - Sequence analysis
+  - Genotyping
+  - Statistical calculation
+  edam-topics:
+  - Sequence analysis
+  - Genetic variation
+  - Sequencing
+  - Workflows
   galaxy: ''
   homepage: https://software.broadinstitute.org/gatk/
   id: gatk
@@ -7710,11 +7114,9 @@
   bunya: ''
   description: Cleaning aligned sequences.
   edam-operations:
-  - term: Sequence alignment analysis
-    url: http://edamontology.org/operation_0258
+  - Sequence alignment analysis
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'Gblocks: Selection of conserved blocks from multiple alignments
       for their use in phylogenetic analysis'
@@ -7747,11 +7149,9 @@
     GREML method), and has subsequently extended for many other analyses to better
     understand the genetic architecture of complex traits.
   edam-operations:
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
+  - Genetic variation analysis
   edam-topics:
-  - term: GWAS study
-    url: http://edamontology.org/topic_3517
+  - GWAS study
   galaxy: ''
   homepage: http://cnsgenomics.com/software/gcta/
   id: gcta
@@ -7773,11 +7173,9 @@
     results (equivalent to MUMmer) with controlled memory consumption and comparable
     or faster execution times particularly with long sequences.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
+  - Sequence analysis
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'Gecko: Ungapped genome comparison'
     title: Gecko 1.2
@@ -7805,13 +7203,10 @@
     a simple, flexible, and powerful system for exploring genetic variation for disease
     and population genetics.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
+  - Sequence analysis
+  - Genetic variation analysis
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'GEMINI actionable_mutations: Retrieve genes with actionable somatic
       mutations via COSMIC and DGIdb'
@@ -7914,13 +7309,10 @@
     acid sequence and intron position conservation. In addition, it allows to incorporate
     RNA-seq evidence for splice site prediction.
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Genome annotation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Homology modeling
-    url: http://edamontology.org/topic_2275
+  - Genomics
+  - Homology modeling
   galaxy: ''
   homepage: http://www.jstacs.de/index.php/GeMoMa
   id: gemoma
@@ -8051,17 +7443,12 @@
     and polyploid genomes | Average k-mer coverage for polyploid genome | Upload results
     from running Jellyfish or KMC
   edam-operations:
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
+  - Genotyping
+  - k-mer counting
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Mathematics
-    url: http://edamontology.org/topic_3315
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Sequence assembly
+  - Mathematics
+  - Mapping
   galaxy:
   - description: 'GenomeScope: reference-free genome profiling'
     title: GenomeScope 2.0+galaxy2
@@ -8086,13 +7473,10 @@
   bunya: ''
   description: Free collection of bioinformatics tools for genome informatics.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
+  - Sequence analysis
   edam-topics:
-  - term: Nucleic acid sites, features and motifs
-    url: http://edamontology.org/topic_3511
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Nucleic acid sites, features and motifs
+  - Sequence analysis
   galaxy: ''
   homepage: http://genometools.org/
   id: genometools
@@ -8160,27 +7544,17 @@
 
     This toolkit assemblies organelle genome from genomic skimming data.'
   edam-operations:
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Mapping assembly
-    url: http://edamontology.org/operation_0523
-  - term: Mapping
-    url: http://edamontology.org/operation_2429
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  edam-topics:
-  - term: Cell biology
-    url: http://edamontology.org/topic_2229
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Plant biology
-    url: http://edamontology.org/topic_0780
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
+  - De-novo assembly
+  - Genome assembly
+  - Mapping assembly
+  - Mapping
+  - Sequence trimming
+  edam-topics:
+  - Cell biology
+  - Sequence assembly
+  - Whole genome sequencing
+  - Plant biology
+  - Model organisms
   galaxy:
   - description: 'Get organelle from reads: '
     title: Get organelle from reads 1.7.7.1+galaxy0
@@ -8228,11 +7602,9 @@
     and simultaneous genome assembly file manipulation. gfastats also allows seamless
     fasta/fastq/gfa conversion.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: Computational biology
-    url: http://edamontology.org/topic_3307
+  - Computational biology
   galaxy:
   - description: 'gfastats: the swiss army knife for genome assembly'
     title: gfastats 1.3.6+galaxy0
@@ -8296,13 +7668,10 @@
   description: Program for comparing, annotating, merging and tracking transcripts
     in GFF files.
   edam-operations:
-  - term: Sequence annotation
-    url: http://edamontology.org/operation_0361
+  - Sequence annotation
   edam-topics:
-  - term: Nucleic acids
-    url: http://edamontology.org/topic_0077
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Nucleic acids
+  - Sequence analysis
   galaxy:
   - description: 'GffCompare: compare assembled transcripts to a reference annotation'
     title: GffCompare 0.12.6+galaxy0
@@ -8345,13 +7714,10 @@
   - 0.12.7-gcccore-10.3.0
   description: program for filtering, converting and manipulating GFF files
   edam-operations:
-  - term: Sequence annotation
-    url: http://edamontology.org/operation_0361
+  - Sequence annotation
   edam-topics:
-  - term: Nucleic acids
-    url: http://edamontology.org/topic_0077
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Nucleic acids
+  - Sequence analysis
   galaxy:
   - description: 'gffread: Filters and/or converts GFF3/GTF2 records'
     title: gffread 2.2.1.4+galaxy0
@@ -8373,11 +7739,9 @@
   bunya: ''
   description: Plotting system for R, based on the grammar of graphics.
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Visualisation
   edam-topics:
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
+  - Data visualisation
   galaxy:
   - description: 'heatmap2: '
     title: heatmap2 3.1.3.1+galaxy0
@@ -8457,13 +7821,10 @@
   - 2023.04.28
   description: Genomic Mapping and Alignment Program for mRNA and EST Sequences.
   edam-operations:
-  - term: Genetic mapping
-    url: http://edamontology.org/operation_0282
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Genetic mapping
+  - Sequence alignment
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Mapping
   galaxy: ''
   homepage: http://research-pub.gene.com/gmap/
   id: gmap
@@ -8492,8 +7853,7 @@
     also be a command that reads from a pipe. GNU parallel can then split the input
     and pipe it into commands in parallel.
   edam-operations:
-  - term: Splitting
-    url: http://edamontology.org/operation_3359
+  - Splitting
   edam-topics: ''
   galaxy: ''
   homepage: https://www.gnu.org/software/parallel/
@@ -8544,11 +7904,9 @@
     \ in the set of enriched GO terms and simplify its output.\nIt was developed by\
     \ the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ci\xEAncia."
   edam-operations:
-  - term: Gene-set enrichment analysis
-    url: http://edamontology.org/operation_2436
+  - Gene-set enrichment analysis
   edam-topics:
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - Transcriptomics
   galaxy:
   - description: 'GOEnrichment: performs GO enrichment analysis of a set of gene products'
     title: GOEnrichment 2.0.1
@@ -8574,11 +7932,9 @@
   description: Detect Gene Ontology and/or other user defined categories which are
     over/under represented in RNA-seq data.
   edam-operations:
-  - term: Gene functional annotation
-    url: http://edamontology.org/operation_3672
+  - Gene functional annotation
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - RNA-Seq
   galaxy:
   - description: 'goseq: tests for overrepresented gene categories'
     title: goseq 1.50.0+galaxy0
@@ -8625,23 +7981,15 @@
     informative, and publication-ready representations of phylogenetically- and taxonomically-driven
     investigation.
   edam-operations:
-  - term: Phylogenetic inference
-    url: http://edamontology.org/operation_0323
-  - term: Phylogenetic tree visualisation
-    url: http://edamontology.org/operation_0567
-  - term: Phylogenetic tree editing
-    url: http://edamontology.org/operation_0326
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
-  - term: Cladistics
-    url: http://edamontology.org/topic_3944
+  - Phylogenetic inference
+  - Phylogenetic tree visualisation
+  - Phylogenetic tree editing
+  - Taxonomic classification
+  edam-topics:
+  - Metagenomics
+  - Phylogenetics
+  - Phylogenomics
+  - Cladistics
   galaxy:
   - description: 'GraPhlAn: to produce graphical output of an input tree'
     title: GraPhlAn 1.1.3
@@ -8674,11 +8022,9 @@
     fast at calculating the nonbonded interactions (that usually dominate simulations)
     many groups are also using it for research on non-biological systems, e.g. polymers.
   edam-operations:
-  - term: Molecular dynamics
-    url: http://edamontology.org/operation_2476
+  - Molecular dynamics
   edam-topics:
-  - term: Molecular dynamics
-    url: http://edamontology.org/topic_0176
+  - Molecular dynamics
   galaxy:
   - description: 'Modify/convert and concatate GROMACS trajectories: using trjconv
       and trjcat'
@@ -8786,25 +8132,16 @@
     samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk
     is open source and released under the GNU General Public License (Version 3).'
   edam-operations:
-  - term: Genome alignment
-    url: http://edamontology.org/operation_3182
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Query and retrieval
-    url: http://edamontology.org/operation_0224
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Database management
-    url: http://edamontology.org/topic_3489
-  - term: Proteins
-    url: http://edamontology.org/topic_0078
+  - Genome alignment
+  - Taxonomic classification
+  - Sequence assembly
+  - Query and retrieval
+  edam-topics:
+  - Metagenomics
+  - Taxonomy
+  - Phylogenetics
+  - Database management
+  - Proteins
   galaxy:
   - description: 'GTDB-Tk Classify genomes: by placement in GTDB reference tree'
     title: GTDB-Tk Classify genomes 2.3.2+galaxy1
@@ -8871,19 +8208,13 @@
   description: Gubbins is a tool for rapid phylogenetic analysis of large samples
     of recombinant bacterial whole genome sequences.
   edam-operations:
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Phylogenetic inference
-    url: http://edamontology.org/operation_0323
-  - term: Ancestral reconstruction
-    url: http://edamontology.org/operation_3745
+  - Genotyping
+  - Phylogenetic inference
+  - Ancestral reconstruction
   edam-topics:
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
-  - term: Genotype and phenotype
-    url: http://edamontology.org/topic_0625
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
+  - Phylogeny
+  - Genotype and phenotype
+  - Whole genome sequencing
   galaxy:
   - description: 'Gubbins: Recombination detection in Bacteria'
     title: Gubbins 3.2.1+galaxy0
@@ -8933,10 +8264,8 @@
 
     The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md'
   edam-operations:
-  - term: Haplotype mapping
-    url: http://edamontology.org/operation_0487
-  - term: Variant classification
-    url: http://edamontology.org/operation_3225
+  - Haplotype mapping
+  - Variant classification
   edam-topics: ''
   galaxy:
   - description: 'Hapcut2: - haplotype assembly for diploid organisms'
@@ -8979,15 +8308,11 @@
   bunya: ''
   description: Tool for single-species active module discovery.
   edam-operations:
-  - term: Pathway or network analysis
-    url: http://edamontology.org/operation_2497
+  - Pathway or network analysis
   edam-topics:
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
+  - Genetics
+  - Gene expression
+  - Molecular interactions, pathways and networks
   galaxy:
   - description: 'Calculate a Heinz score: for each node'
     title: Calculate a Heinz score 1.0
@@ -9021,17 +8346,12 @@
   description: This tool provides functional annotation for a list of genes by connecting
     with DAVID database.
   edam-operations:
-  - term: Database search
-    url: http://edamontology.org/operation_2421
-  - term: Service invocation
-    url: http://edamontology.org/operation_3763
-  - term: Gene functional annotation
-    url: http://edamontology.org/operation_3672
+  - Database search
+  - Service invocation
+  - Gene functional annotation
   edam-topics:
-  - term: Ontology and terminology
-    url: http://edamontology.org/topic_0089
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
+  - Ontology and terminology
+  - Gene expression
   galaxy:
   - description: 'DAVID: functional annotation for a list of genes'
     title: DAVID 1.0.1
@@ -9061,21 +8381,14 @@
   description: This tool can be used to analyze the patterns of linkage disequilibrium
     (LD) between polymorphic sites in a locus.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Linkage disequilibrium calculation
-    url: http://edamontology.org/operation_0488
-  - term: Variant pattern analysis
-    url: http://edamontology.org/operation_3504
-  edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Data mining
-    url: http://edamontology.org/topic_3473
+  - Data handling
+  - Linkage disequilibrium calculation
+  - Variant pattern analysis
+  edam-topics:
+  - Mapping
+  - Molecular interactions, pathways and networks
+  - DNA polymorphism
+  - Data mining
   galaxy:
   - description: 'LD: linkage disequilibrium and tag SNPs'
     title: LD 1.0.0
@@ -9105,19 +8418,13 @@
   description: This tool creates a link to the g:GOSt tool (Gene Group Functional
     Profiling), which provides functional profiling of gene lists.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Service invocation
-    url: http://edamontology.org/operation_3763
-  - term: Gene functional annotation
-    url: http://edamontology.org/operation_3672
+  - Data handling
+  - Service invocation
+  - Gene functional annotation
   edam-topics:
-  - term: Ontology and terminology
-    url: http://edamontology.org/topic_0089
-  - term: Function analysis
-    url: http://edamontology.org/topic_1775
-  - term: Data mining
-    url: http://edamontology.org/topic_3473
+  - Ontology and terminology
+  - Function analysis
+  - Data mining
   galaxy:
   - description: 'g:Profiler: tools for functional profiling of gene lists'
     title: g:Profiler 1.0.0
@@ -9149,23 +8456,15 @@
     \ 3.6 documentation.\n\nscHiCExplorer \u2014 scHiCExplorer 7 documentation.\n\n\
     Free document hosting provided by Read the Docs."
   edam-operations:
-  - term: Validation
-    url: http://edamontology.org/operation_2428
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  edam-topics:
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Chromosome conformation capture
-    url: http://edamontology.org/topic_3940
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
-  - term: Epigenetics
-    url: http://edamontology.org/topic_3295
+  - Validation
+  - Visualisation
+  - Standardisation and normalisation
+  edam-topics:
+  - Workflows
+  - DNA
+  - Chromosome conformation capture
+  - ChIP-seq
+  - Epigenetics
   galaxy:
   - description: 'hicPCA: compute the principal components for A / B compartment analysis'
     title: hicPCA 3.7.2+galaxy0
@@ -9204,23 +8503,15 @@
   description: Remove CCS reads with remnant PacBio adapter sequences and convert
     outputs to a compressed .fastq (.fastq.gz).
   edam-operations:
-  - term: Primer removal
-    url: http://edamontology.org/operation_3237
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Agricultural science
-    url: http://edamontology.org/topic_3810
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
+  - Primer removal
+  - De-novo assembly
+  - Genome assembly
+  - Sequence trimming
+  edam-topics:
+  - Sequence assembly
+  - Agricultural science
+  - Workflows
+  - Whole genome sequencing
   galaxy:
   - description: 'HiFi Adapter Filter: Remove CCS reads with remnant PacBio adapter
       sequences'
@@ -9248,13 +8539,10 @@
   - 0.16.1-gcccore-10.3.0
   description: 'Hifiasm: a haplotype-resolved assembler for accurate Hifi reads'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
+  - Genome assembly
+  - De-novo assembly
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'Hifiasm: haplotype-resolved de novo assembler for PacBio Hifi reads'
     title: Hifiasm 0.19.8+galaxy1
@@ -9308,11 +8596,9 @@
     DNA and RNA) to a population of human genomes (as well as to a single reference
     genome).
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence alignment
   edam-topics:
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
+  - RNA-seq
   galaxy:
   - description: 'HISAT2: A fast and sensitive alignment program'
     title: HISAT2 2.2.1+galaxy1
@@ -9386,15 +8672,11 @@
     using probabilistic models called profile hidden Markov models. The new HMMER3
     project, HMMER is now as fast as BLAST for protein search.
   edam-operations:
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Formatting
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
-  - term: Gene and protein families
-    url: http://edamontology.org/topic_0623
+  - Sequence analysis
+  - Sequence sites, features and motifs
+  - Gene and protein families
   galaxy:
   - description: 'hmmconvert: convert profile file to a HMMER format'
     title: hmmconvert 0.1.0
@@ -9462,8 +8744,7 @@
     learning fast and easy to use.
   edam-operations: ''
   edam-topics:
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
+  - Machine learning
   galaxy: ''
   homepage: https://github.com/horovod/horovod
   id: horovod
@@ -9485,11 +8766,9 @@
   description: Python framework to process and analyse high-throughput sequencing
     (HTS) data
   edam-operations:
-  - term: Nucleic acid sequence analysis
-    url: http://edamontology.org/operation_2478
+  - Nucleic acid sequence analysis
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'htseq-count: - Count aligned reads in a BAM file that overlap features
       in a GFF file'
@@ -9519,11 +8798,9 @@
     reference data in FASTA format and tab-delimited files with genomic coordinates.
     It is utilized and incorporated into both SAMtools and BCFtools.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Data management
   galaxy: ''
   homepage: http://www.htslib.org/
   id: htslib
@@ -9554,17 +8831,12 @@
     \ profiling answers the question \u201CWhat are the microbes in my community-of-interest\
     \ doing (or are capable of doing)?\u201D"
   edam-operations:
-  - term: Species frequency estimation
-    url: http://edamontology.org/operation_3221
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
-  - term: Phylogenetic analysis
-    url: http://edamontology.org/operation_0324
+  - Species frequency estimation
+  - Taxonomic classification
+  - Phylogenetic analysis
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
+  - Metagenomics
+  - Phylogenomics
   galaxy:
   - description: 'Join (merge): gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables
       into a single table'
@@ -9629,8 +8901,7 @@
     \ functional profiling answers the question \u201CWhat are the microbes in my\
     \ community-of-interest doing (or capable of doing)?\u201D"
   edam-operations:
-  - term: Metabolic pathway prediction
-    url: http://edamontology.org/operation_3929
+  - Metabolic pathway prediction
   edam-topics: ''
   galaxy:
   - description: 'HUMAnN2: to profile presence/absence and abundance of microbial
@@ -9692,15 +8963,11 @@
   description: Software package for the analysis of genetic sequences using techniques
     in phylogenetics, molecular evolution, and machine learning.
   edam-operations:
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
+  - Statistical calculation
   edam-topics:
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
+  - Phylogeny
+  - Small molecules
+  - Molecular interactions, pathways and networks
   galaxy:
   - description: 'HyPhy-aBSREL: adaptive Branch Site Random Effects Likelihood'
     title: HyPhy-aBSREL 2.5.47+galaxy0
@@ -9771,13 +9038,10 @@
     HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi
     reads to produce high-quality phased genome assemblies
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Phasing
-    url: http://edamontology.org/operation_3454
+  - Genome assembly
+  - Phasing
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy: ''
   homepage: https://github.com/PacificBiosciences/pbipa
   id: pbipa
@@ -9803,13 +9067,10 @@
     is more capable of identifying RNA homologs that conserve their secondary structure
     more than their primary sequence.
   edam-operations:
-  - term: Nucleic acid feature detection
-    url: http://edamontology.org/operation_0415
+  - Nucleic acid feature detection
   edam-topics:
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
-  - term: Structural genomics
-    url: http://edamontology.org/topic_0122
+  - Sequence sites, features and motifs
+  - Structural genomics
   galaxy:
   - description: 'cmscan: Search sequences against collections of covariance models'
     title: cmscan 1.1.4+galaxy0
@@ -9870,15 +9131,11 @@
     including short-read alignments in the SAM/BAM format. Data can be viewed from
     local files or over the web via http.
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Visualisation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Genomics
+  - Data visualisation
+  - Sequence analysis
   galaxy: ''
   homepage: http://www.broadinstitute.org/igv/
   id: igv
@@ -9905,23 +9162,15 @@
   bunya: ''
   description: A tool to detect Integron in DNA sequences.
   edam-operations:
-  - term: Nucleic acid feature detection
-    url: http://edamontology.org/operation_0415
-  - term: Sequence motif recognition
-    url: http://edamontology.org/operation_0239
-  - term: Protein feature detection
-    url: http://edamontology.org/operation_3092
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  edam-topics:
-  - term: Functional genomics
-    url: http://edamontology.org/topic_0085
-  - term: Mobile genetic elements
-    url: http://edamontology.org/topic_0798
-  - term: Molecular biology
-    url: http://edamontology.org/topic_3047
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Nucleic acid feature detection
+  - Sequence motif recognition
+  - Protein feature detection
+  - Genome annotation
+  edam-topics:
+  - Functional genomics
+  - Mobile genetic elements
+  - Molecular biology
+  - Sequence analysis
   galaxy:
   - description: 'Integron Finder: is a program that detects integrons in DNA sequences'
     title: Integron Finder 2.0.3+galaxy0
@@ -9991,15 +9240,11 @@
   - 5.55-88.0-foss-2021a
   description: Scan sequences against the InterPro protein signature databases.
   edam-operations:
-  - term: Sequence motif recognition
-    url: http://edamontology.org/operation_0239
-  - term: Protein feature detection
-    url: http://edamontology.org/operation_3092
+  - Sequence motif recognition
+  - Protein feature detection
   edam-topics:
-  - term: Gene and protein families
-    url: http://edamontology.org/topic_0623
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Gene and protein families
+  - Sequence analysis
   galaxy:
   - description: 'InterProScan: functional annotation'
     title: InterProScan 5.59-91.0+galaxy3
@@ -10092,19 +9337,13 @@
     \ sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies.\n\
     \nWelcome to ipyrad \u2014 ipyrad documentation."
   edam-operations:
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: de Novo sequencing
-    url: http://edamontology.org/operation_3644
-  - term: Haplotype mapping
-    url: http://edamontology.org/operation_0487
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Population genetics
-    url: http://edamontology.org/topic_3056
+  - Sequence assembly
+  - de Novo sequencing
+  - Haplotype mapping
+  edam-topics:
+  - Sequence assembly
+  - Phylogenetics
+  - Population genetics
   galaxy: ''
   homepage: https://github.com/dereneaton/ipyrad/
   id: ipyrad
@@ -10129,15 +9368,11 @@
     It is based on the IQPNNI algorithm with 10-fold speedup together with substantially
     additional features.
   edam-operations:
-  - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
-    url: http://edamontology.org/operation_0547
+  - Phylogenetic tree generation (maximum likelihood and Bayesian methods)
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
+  - Phylogenetics
+  - Statistics and probability
+  - Phylogenomics
   galaxy:
   - description: 'IQ-TREE: Phylogenomic / evolutionary tree construction from multiple
       sequences'
@@ -10166,13 +9401,10 @@
     in a SingleCellExperiment object with visualization of dimensionality reduction
     results.
   edam-operations:
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
+  - Clustering
   edam-topics:
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - Gene expression
+  - Transcriptomics
   galaxy:
   - description: 'iSEE: '
     title: iSEE 1.0.0
@@ -10197,17 +9429,12 @@
   description: Automated identification of insertion sequence elements in prokaryotic
     genomes.
   edam-operations:
-  - term: Structural variation detection
-    url: http://edamontology.org/operation_3228
+  - Structural variation detection
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: DNA structural variation
-    url: http://edamontology.org/topic_3175
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
+  - Genomics
+  - DNA structural variation
+  - Sequence analysis
+  - Genetic variation
   galaxy:
   - description: 'ISEScan: Insertion Sequence Elements detection in prokaryotic genomes'
     title: ISEScan 1.7.2.3+galaxy1
@@ -10235,15 +9462,11 @@
     supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but
     other transcript qunatification tools are easy to import as well.
   edam-operations:
-  - term: Sequence comparison
-    url: http://edamontology.org/operation_2451
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
+  - Sequence comparison
+  - Sequence analysis
   edam-topics:
-  - term: Computational biology
-    url: http://edamontology.org/topic_3307
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
+  - Computational biology
+  - Gene transcripts
   galaxy:
   - description: 'IsoformSwitchAnalyzeR: statistical identification of isoform switching'
     title: IsoformSwitchAnalyzeR 1.20.0+galaxy5
@@ -10270,19 +9493,13 @@
     the IsoSeq GUI-based analysis application. A composable workflow of existing tools
     and algorithms, combined with a new clustering technique.
   edam-operations:
-  - term: Demultiplexing
-    url: http://edamontology.org/operation_3933
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
-  - term: Primer removal
-    url: http://edamontology.org/operation_3237
-  - term: DNA barcoding
-    url: http://edamontology.org/operation_3200
-  edam-topics:
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
+  - Demultiplexing
+  - Sequence trimming
+  - Clustering
+  - Primer removal
+  - DNA barcoding
+  edam-topics:
+  - Gene transcripts
   galaxy: ''
   homepage: https://github.com/PacificBiosciences/IsoSeq
   id: isoseq3
@@ -10304,19 +9521,13 @@
 
     iVar - DataBase of Genomics Variants.'
   edam-operations:
-  - term: Variant classification
-    url: http://edamontology.org/operation_3225
-  - term: Text annotation
-    url: http://edamontology.org/operation_3778
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
+  - Variant classification
+  - Text annotation
+  - Variant calling
   edam-topics:
-  - term: Biological databases
-    url: http://edamontology.org/topic_3071
-  - term: Evolutionary biology
-    url: http://edamontology.org/topic_3299
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Biological databases
+  - Evolutionary biology
+  - Sequencing
   galaxy:
   - description: 'ivar consensus: Call consensus from aligned BAM file'
     title: ivar consensus 1.4.2+galaxy0
@@ -10359,11 +9570,9 @@
     of genomic regions (or between a group of genomic regions and a reference center
     of symmetry), and does not require fixing location and scale at the outset.
   edam-operations:
-  - term: Differential gene expression analysis
-    url: http://edamontology.org/operation_3223
+  - Differential gene expression analysis
   edam-topics:
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
+  - Statistics and probability
   galaxy:
   - description: 'IWTomics Load: Smooth and Plot'
     title: IWTomics Load 1.0.0.0
@@ -10396,8 +9605,7 @@
     Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
   edam-operations: ''
   edam-topics:
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
+  - Statistics and probability
   galaxy: ''
   homepage: https://mcmc-jags.sourceforge.io/
   id: jags
@@ -10423,25 +9631,16 @@
     merged variants represents a set of analogous variants occurring in different
     samples.
   edam-operations:
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: Genome indexing
-    url: http://edamontology.org/operation_3211
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  edam-topics:
-  - term: Structural variation
-    url: http://edamontology.org/topic_3175
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - Genotyping
+  - Variant calling
+  - Genome indexing
+  - Visualisation
+  edam-topics:
+  - Structural variation
+  - DNA polymorphism
+  - Workflows
+  - Mapping
+  - RNA-Seq
   galaxy: ''
   homepage: https://github.com/mkirsche/Jasmine
   id: jasminesv
@@ -10503,11 +9702,9 @@
     for visualization of genome data. Being developed by the GMOD project as a successor
     to GBrowse.
   edam-operations:
-  - term: Genome visualisation
-    url: http://edamontology.org/operation_3208
+  - Genome visualisation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy:
   - description: 'JBrowse: genome browser'
     title: JBrowse 1.16.11+galaxy1
@@ -10557,13 +9754,10 @@
   - 2.3.0-gcc-11.3.0                (D)
   description: A command-line algorithm for counting k-mers in DNA sequence.
   edam-operations:
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
+  - k-mer counting
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Sequence analysis
+  - Genomics
   galaxy:
   - description: 'jellyfish: '
     title: jellyfish 2.3.0+galaxy1
@@ -10632,19 +9826,13 @@
     this distribution, we include the pipeline for generating Hi-C maps from fastq
     raw data files and command line tools for feature annotation on the Hi-C maps.
   edam-operations:
-  - term: Genome indexing
-    url: http://edamontology.org/operation_3211
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Epigenetics
-    url: http://edamontology.org/topic_3295
+  - Genome indexing
+  - Visualisation
+  edam-topics:
+  - Sequencing
+  - Mapping
+  - Genomics
+  - Epigenetics
   galaxy: ''
   homepage: https://github.com/aidenlab/juicer
   id: juicer
@@ -10690,15 +9878,11 @@
     It is based on the novel idea of pseudoalignment for rapidly determining the compatibility
     of reads with targets, without the need for alignment.
   edam-operations:
-  - term: Gene expression profiling
-    url: http://edamontology.org/operation_0314
+  - Gene expression profiling
   edam-topics:
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
+  - Transcriptomics
+  - RNA-seq
+  - Gene expression
   galaxy:
   - description: 'Kallisto pseudo: run pseudoalignment on RNA-Seq transcripts'
     title: Kallisto pseudo 0.48.0+galaxy1
@@ -10725,15 +9909,11 @@
   description: Suite of tools that generate, analyse and compare k-mer spectra produced
     from sequence files
   edam-operations:
-  - term: Sequence composition calculation
-    url: http://edamontology.org/operation_0236
-  - term: Sequence feature detection
-    url: http://edamontology.org/operation_0253
+  - Sequence composition calculation
+  - Sequence feature detection
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Sequence analysis
+  - Genomics
   galaxy: ''
   homepage: http://www.earlham.ac.uk/kat-tools
   id: kat
@@ -10777,11 +9957,9 @@
     de novo assemblies faster, and sometimes better. khmer can also identify (and
     fix) problems with shotgun data.
   edam-operations:
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
+  - Standardisation and normalisation
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'khmer: Abundance Distribution: Calculate abundance distribution
       of k-mers using pre-made k-mer countgraphs'
@@ -10839,15 +10017,11 @@
   description: KMC is a utility designed for counting k-mers (sequences of consecutive
     k symbols) in a set of reads from genome sequencing projects.
   edam-operations:
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
+  - k-mer counting
   edam-topics:
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Whole genome sequencing
+  - Genomics
+  - Sequence assembly
   galaxy: ''
   homepage: http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about
   id: kmc
@@ -10893,13 +10067,10 @@
     and high speed by utilizing exact alignments of k-mers and a novel classification
     algorithm.
   edam-operations:
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
+  - Taxonomic classification
   edam-topics:
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Taxonomy
+  - Metagenomics
   galaxy:
   - description: 'Convert Kraken: data to Galaxy taxonomy representation'
     title: Convert Kraken 1.2+galaxy0
@@ -10953,13 +10124,10 @@
     common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments
     inform the classification algorithm.
   edam-operations:
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
+  - Taxonomic classification
   edam-topics:
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Taxonomy
+  - Metagenomics
   galaxy:
   - description: 'Kraken2: assign taxonomic labels to sequencing reads'
     title: Kraken2 2.1.1+galaxy1
@@ -10983,13 +10151,10 @@
   description: KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq
     output files
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Visualisation
   edam-topics:
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Taxonomy
+  - Metagenomics
   galaxy:
   - description: 'Krakentools: Combine multiple Kraken reports: into a combined report
       file'
@@ -11023,11 +10188,9 @@
   description: Krona creates interactive HTML5 charts of hierarchical data (such as
     taxonomic abundance in a metagenome).
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Visualisation
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Metagenomics
   galaxy:
   - description: 'Krona pie chart: from taxonomic profile'
     title: Krona pie chart 2.7.1+galaxy0
@@ -11079,21 +10242,14 @@
     Welcome to LAMA, an open source pipeline to automatically identify embryo dysmorphology
     from 3D volumetric images.'
   edam-operations:
-  - term: Image analysis
-    url: http://edamontology.org/operation_3443
-  - term: Image annotation
-    url: http://edamontology.org/operation_3553
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  edam-topics:
-  - term: Tomography
-    url: http://edamontology.org/topic_3452
-  - term: Genotype and phenotype
-    url: http://edamontology.org/topic_0625
-  - term: MRI
-    url: http://edamontology.org/topic_3444
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - Image analysis
+  - Image annotation
+  - Standardisation and normalisation
+  edam-topics:
+  - Tomography
+  - Genotype and phenotype
+  - MRI
+  - Workflows
   galaxy: ''
   homepage: https://github.com/mpi2/LAMA
   id: lama
@@ -11117,13 +10273,10 @@
   description: A tool for (1) aligning two DNA sequences, and (2) inferring appropriate
     scoring parameters automatically.
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
+  - Sequence alignment
+  - Read mapping
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy:
   - description: 'LASTZ_D: : estimate substitution scores matrix'
     title: LASTZ_D 1.04.22+galaxy0
@@ -11215,13 +10368,10 @@
   description: Data analysis, linear models and differential expression for microarray
     data.
   edam-operations:
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
+  - RNA-Seq analysis
   edam-topics:
-  - term: Molecular biology
-    url: http://edamontology.org/topic_3047
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
+  - Molecular biology
+  - Genetics
   galaxy:
   - description: 'limma: Perform differential expression with limma-voom or limma-trend'
     title: limma 3.58.1+galaxy0
@@ -11249,23 +10399,15 @@
     assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes,
     etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.
   edam-operations:
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Scaffolding
+  - Genome assembly
+  - Read mapping
+  - Read pre-processing
+  - Sequence trimming
+  edam-topics:
+  - Sequence assembly
+  - Mapping
+  - Sequencing
   galaxy:
   - description: 'LINKS: - scaffold genome assemblies with long reads'
     title: LINKS 2.0.1+galaxy+1
@@ -11293,13 +10435,10 @@
     (e.g. mapping or base/indel alignment uncertainty), which are usually ignored
     by other methods or only used for filtering.
   edam-operations:
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
+  - Variant calling
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
+  - Genomics
+  - Genetic variation
   galaxy:
   - description: 'Add LoFreq alignment quality scores: to aligned read SAM/BAM records'
     title: Add LoFreq alignment quality scores 2.1.5+galaxy1
@@ -11341,11 +10480,9 @@
     Currently, it only calls single nucleotide variants (SNVs), but it can genotype
     indels if they are given in an input VCF.
   edam-operations:
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
+  - Variant calling
   edam-topics:
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
+  - Genetic variation
   galaxy: ''
   homepage: https://github.com/pjedge/longshot
   id: longshot
@@ -11390,11 +10527,9 @@
     of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this
     package.
   edam-operations:
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
+  - Sequence assembly
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy: ''
   homepage: https://github.com/oushujun/LTR_retriever
   id: ltr_retriever
@@ -11437,19 +10572,13 @@
   - 2.2.9.1
   description: Model-based Analysis of ChIP-seq data.
   edam-operations:
-  - term: Peak calling
-    url: http://edamontology.org/operation_3222
-  - term: Enrichment analysis
-    url: http://edamontology.org/operation_3501
-  - term: Gene regulatory network analysis
-    url: http://edamontology.org/operation_1781
+  - Peak calling
+  - Enrichment analysis
+  - Gene regulatory network analysis
   edam-topics:
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
+  - ChIP-seq
+  - Molecular interactions, pathways and networks
+  - Transcription factors and regulatory sites
   galaxy:
   - description: 'MACS2 bdgdiff: Differential peak detection based on paired four
       bedgraph files'
@@ -11756,11 +10885,9 @@
   description: MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed
     multiple sequence alignment program.
   edam-operations:
-  - term: Multiple sequence alignment
-    url: http://edamontology.org/operation_0492
+  - Multiple sequence alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'MAFFT: Multiple alignment program for amino acid or nucleotide sequences'
     title: MAFFT 7.520+galaxy0
@@ -11802,15 +10929,11 @@
   description: Computational tool to identify important genes from the recent genome-scale
     CRISPR-Cas9 knockout screens technology.
   edam-operations:
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
+  - Genetic variation analysis
   edam-topics:
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genetics
+  - Genetic variation
+  - Genomics
   galaxy:
   - description: 'MAGeCK count: - collect sgRNA read counts from read mapping files'
     title: MAGeCK count 0.5.9.2.4
@@ -11851,15 +10974,11 @@
     s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently\
     \ annotate their genomes and to create genome databases."
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Genome annotation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Genomics
+  - DNA
+  - Sequence analysis
   galaxy:
   - description: 'Maker: genome annotation pipeline'
     title: Maker 2.31.11+galaxy2
@@ -11895,21 +11014,14 @@
     peak-clipping algorithm (SNIP), peak alignment using warping functions, handling
     of replicated measurements as well as allowing spectra with different resolutions.
   edam-operations:
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Spectrum calculation
-    url: http://edamontology.org/operation_3860
-  - term: Peak detection
-    url: http://edamontology.org/operation_3215
-  - term: Mass spectra calibration
-    url: http://edamontology.org/operation_3627
-  edam-topics:
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
+  - Quantification
+  - Visualisation
+  - Spectrum calculation
+  - Peak detection
+  - Mass spectra calibration
+  edam-topics:
+  - Proteomics experiment
+  - Proteomics
   galaxy:
   - description: 'MALDIquant peak detection: Peak detection, binning and filtering
       for mass-spectrometry imaging data'
@@ -11939,19 +11051,13 @@
   - 2.3-gcc-10.3.0
   description: Fast genome and metagenome distance estimation using MinHash.
   edam-operations:
-  - term: Sequence distance matrix generation
-    url: http://edamontology.org/operation_0289
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: DNA mutation
-    url: http://edamontology.org/topic_2533
+  - Sequence distance matrix generation
+  edam-topics:
+  - Genomics
+  - Metagenomics
+  - Statistics and probability
+  - Sequence analysis
+  - DNA mutation
   galaxy: ''
   homepage: https://github.com/marbl/mash
   id: mash
@@ -12039,15 +11145,11 @@
     \ assemble data sets containing only short reads from Illumina sequencing or a\
     \ mixture of short reads and long reads (Sanger, 454)."
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
+  - Genome assembly
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence assembly
+  - Whole genome sequencing
+  - Sequence analysis
   galaxy:
   - description: 'MaSuRCA simple: The MaSuRCA (Maryland Super Read Cabog Assembler)
       genome assembly and analysis toolkit without config'
@@ -12071,15 +11173,11 @@
   bunya: ''
   description: Tool to import, process, clean, and compare mass spectrometry data.
   edam-operations:
-  - term: Spectral library search
-    url: http://edamontology.org/operation_3801
-  - term: Format validation
-    url: http://edamontology.org/operation_0336
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
+  - Spectral library search
+  - Format validation
+  - Filtering
   edam-topics:
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Metabolomics
   galaxy:
   - description: 'matchms convert: convert between mass spectral library formats (.mgf/.msp/.json)
       using matchms'
@@ -12141,10 +11239,8 @@
     and interactive visualizations in Python. Matplotlib makes easy things easy and
     hard things possible.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Data handling
+  - Visualisation
   edam-topics: ''
   galaxy: ''
   homepage: https://matplotlib.org/
@@ -12164,15 +11260,11 @@
   description: Software for binning assembled metagenomic sequences based on an Expectation-Maximization
     algorithm.
   edam-operations:
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
+  - Sequence assembly
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Microbiology
-    url: http://edamontology.org/topic_3301
+  - Metagenomics
+  - Sequence assembly
+  - Microbiology
   galaxy:
   - description: 'MaxBin2: clusters metagenomic contigs into bins'
     title: MaxBin2 2.2.7+galaxy2
@@ -12197,29 +11289,18 @@
   description: Quantitative proteomics software package designed for analyzing large
     mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.
   edam-operations:
-  - term: Imputation
-    url: http://edamontology.org/operation_3557
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Protein quantification
-    url: http://edamontology.org/operation_3630
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  - term: Heat map generation
-    url: http://edamontology.org/operation_0531
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
-  - term: Principal component plotting
-    url: http://edamontology.org/operation_2939
-  edam-topics:
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
+  - Imputation
+  - Visualisation
+  - Protein quantification
+  - Statistical calculation
+  - Standardisation and normalisation
+  - Heat map generation
+  - Clustering
+  - Principal component plotting
+  edam-topics:
+  - Proteomics experiment
+  - Proteomics
+  - Statistics and probability
   galaxy:
   - description: 'MaxQuant (using mqpar.xml): '
     title: MaxQuant (using mqpar.xml) 2.0.3.0+galaxy0
@@ -12257,15 +11338,11 @@
   description: MCL is a clustering algorithm widely used in bioinformatics and gaining
     traction in other fields.
   edam-operations:
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
-  - term: Network analysis
-    url: http://edamontology.org/operation_3927
-  - term: Gene regulatory network analysis
-    url: http://edamontology.org/operation_1781
+  - Clustering
+  - Network analysis
+  - Gene regulatory network analysis
   edam-topics:
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
+  - Molecular interactions, pathways and networks
   galaxy: ''
   homepage: http://micans.org/mcl/
   id: mcl
@@ -12290,11 +11367,9 @@
     supported coordinate formats for the full list). It can write most of these formats,
     too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol
   edam-operations:
-  - term: Molecular dynamics
-    url: http://edamontology.org/operation_2476
+  - Molecular dynamics
   edam-topics:
-  - term: Molecular dynamics
-    url: http://edamontology.org/topic_0176
+  - Molecular dynamics
   galaxy:
   - description: 'Cosine Content: - measure the cosine content of the PCA projection'
     title: Cosine Content 1.0.0+galaxy0
@@ -12345,17 +11420,12 @@
     nanopore sequencing data. This task is performed using neural networks applied
     a pileup of individual sequencing reads against a draft assembly.
   edam-operations:
-  - term: Base-calling
-    url: http://edamontology.org/operation_3185
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
+  - Base-calling
+  - Variant calling
+  - Sequence assembly
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
+  - Sequence assembly
+  - Machine learning
   galaxy:
   - description: 'medaka variant pipeline: via neural networks'
     title: medaka variant pipeline 1.4.4+galaxy1
@@ -12390,17 +11460,12 @@
     such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage,
     whereas its goal is not to make memory usage as low as possible.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
+  - Genome assembly
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Ecology
-    url: http://edamontology.org/topic_0610
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Metagenomics
+  - Sequencing
+  - Ecology
+  - Sequence assembly
   galaxy:
   - description: 'MEGAHIT: for metagenomics assembly'
     title: MEGAHIT 1.2.9+galaxy1
@@ -12455,23 +11520,15 @@
 
     Merqury provides a set of tools for this purpose.'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  - term: Phasing
-    url: http://edamontology.org/operation_3454
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Plant biology
-    url: http://edamontology.org/topic_0780
+  - Genome assembly
+  - k-mer counting
+  - Scaffolding
+  - Phasing
+  - De-novo assembly
+  edam-topics:
+  - Sequence assembly
+  - Whole genome sequencing
+  - Plant biology
   galaxy:
   - description: 'Merqury: evaluate the assembly quality'
     title: Merqury 1.3+galaxy4
@@ -12500,17 +11557,12 @@
     originally developed for use in the Celera Assembler and has since been migrated
     and maintained as part of Canu.
   edam-operations:
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
+  - k-mer counting
   edam-topics:
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Whole genome sequencing
+  - Genomics
+  - Sequence analysis
+  - Sequencing
   galaxy:
   - description: 'Meryl: a genomic k-mer counter and sequence utility'
     title: Meryl 1.3+galaxy6
@@ -12538,19 +11590,13 @@
     composition information and source strain abundance (measured by depth-of-coverage
     by aligning the reads to the contigs) to perform binning
   edam-operations:
-  - term: Read binning
-    url: http://edamontology.org/operation_3798
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Read binning
+  - Sequence assembly
+  - Genome annotation
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Metagenomic sequencing
-    url: http://edamontology.org/topic_3837
+  - Metagenomics
+  - Sequence assembly
+  - Metagenomic sequencing
   galaxy:
   - description: 'MetaBAT2: metagenome binning'
     title: MetaBAT2 2.15+galaxy3
@@ -12607,23 +11653,15 @@
     This history is empty. You can load your own data or get data from an external
     source'
   edam-operations:
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  - term: Sequence merging
-    url: http://edamontology.org/operation_0232
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Metagenomic sequencing
-    url: http://edamontology.org/topic_3837
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Microbial ecology
-    url: http://edamontology.org/topic_3697
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - Read pre-processing
+  - Standardisation and normalisation
+  - Sequence merging
+  edam-topics:
+  - Metagenomics
+  - Metagenomic sequencing
+  - Workflows
+  - Microbial ecology
+  - RNA-Seq
   galaxy:
   - description: 'PEAR Statistics: Generate paired-end reads overlap Statistic from
       PEAR log file'
@@ -12678,13 +11716,10 @@
   description: MetaEuk - sensitive, high-throughput gene discovery and annotation
     for large-scale eukaryotic metagenomics
   edam-operations:
-  - term: Homology-based gene prediction
-    url: http://edamontology.org/operation_3663
+  - Homology-based gene prediction
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Gene and protein families
-    url: http://edamontology.org/topic_0623
+  - Metagenomics
+  - Gene and protein families
   galaxy: ''
   homepage: https://metaeuk.soedinglab.org/
   id: metaeuk
@@ -12708,15 +11743,11 @@
   description: Computational tool for profiling the composition of microbial communities
     from metagenomic shotgun sequencing data.
   edam-operations:
-  - term: Nucleic acid sequence analysis
-    url: http://edamontology.org/operation_2478
-  - term: Phylogenetic tree analysis
-    url: http://edamontology.org/operation_0324
+  - Nucleic acid sequence analysis
+  - Phylogenetic tree analysis
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
+  - Metagenomics
+  - Phylogenomics
   galaxy:
   - description: 'MetaPhlAn: to profile the composition of microbial communities'
     title: MetaPhlAn 4.0.6+galaxy3
@@ -12753,37 +11784,22 @@
     analysis, and clustered heat map visualizations, as well as exploratory analysis
     for a single sample or experimental condition.
   edam-operations:
-  - term: Principal component visualisation
-    url: http://edamontology.org/operation_2939
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Functional clustering
-    url: http://edamontology.org/operation_3459
-  - term: Query and retrieval
-    url: http://edamontology.org/operation_0224
-  - term: Differential protein expression analysis
-    url: http://edamontology.org/operation_3741
-  - term: Heat map generation
-    url: http://edamontology.org/operation_0531
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Indexing
-    url: http://edamontology.org/operation_0227
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
-  - term: Statistical inference
-    url: http://edamontology.org/operation_3658
-  edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Metatranscriptomics
-    url: http://edamontology.org/topic_3941
-  - term: Microbial ecology
-    url: http://edamontology.org/topic_3697
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Principal component visualisation
+  - Visualisation
+  - Functional clustering
+  - Query and retrieval
+  - Differential protein expression analysis
+  - Heat map generation
+  - Quantification
+  - Indexing
+  - Filtering
+  - Statistical inference
+  edam-topics:
+  - Proteomics
+  - Metatranscriptomics
+  - Microbial ecology
+  - Proteomics experiment
+  - Metagenomics
   galaxy:
   - description: 'metaQuantome: database: download the GO, EC, and NCBI databases'
     title: 'metaQuantome: database 2.0.2+galaxy0'
@@ -12827,13 +11843,10 @@
   bunya: ''
   description: Genome assembler for metagenomics datasets.
   edam-operations:
-  - term: Genome alignment
-    url: http://edamontology.org/operation_3182
+  - Genome alignment
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Metagenomics
+  - Sequence analysis
   galaxy:
   - description: 'metaSPAdes: metagenome assembler'
     title: metaSPAdes 3.15.5+galaxy2
@@ -12865,23 +11878,15 @@
     quality control, assembly, visualization, taxonomic profiling, extracting draft
     genomes (binning), and functional annotation.'
   edam-operations:
-  - term: Read binning
-    url: http://edamontology.org/operation_3798
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Demultiplexing
-    url: http://edamontology.org/operation_3933
-  edam-topics:
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Metagenomic sequencing
-    url: http://edamontology.org/topic_3837
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Read binning
+  - Sequence assembly
+  - Genome annotation
+  - Sequence trimming
+  - Demultiplexing
+  edam-topics:
+  - Whole genome sequencing
+  - Metagenomic sequencing
+  - Metagenomics
   galaxy:
   - description: 'MetaWRAP: metagenome binning pipeline'
     title: MetaWRAP 1.3.0+galaxy1
@@ -12906,13 +11911,10 @@
   bunya: ''
   description: A (mostly) universal methylation extractor for BS-seq experiments.
   edam-operations:
-  - term: Sequence alignment conversion
-    url: http://edamontology.org/operation_0260
-  - term: Methylation calling
-    url: http://edamontology.org/operation_3919
+  - Sequence alignment conversion
+  - Methylation calling
   edam-topics:
-  - term: Epigenomics
-    url: http://edamontology.org/topic_3173
+  - Epigenomics
   galaxy:
   - description: 'MethylDackel: A tool for processing bisulfite sequencing alignments'
     title: MethylDackel 0.5.2+galaxy0
@@ -12957,19 +11959,13 @@
     population assuming a migration matrix model with asymmetric migration rates and
     different subpopulation sizes, and population divergences or admixture.
   edam-operations:
-  - term: Haplotype mapping
-    url: http://edamontology.org/operation_0487
-  - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
-    url: http://edamontology.org/operation_0547
-  - term: Cell migration analysis
-    url: http://edamontology.org/operation_3446
-  edam-topics:
-  - term: Population genetics
-    url: http://edamontology.org/topic_3056
-  - term: Nucleic acid structure analysis
-    url: http://edamontology.org/topic_0097
-  - term: Zoology
-    url: http://edamontology.org/topic_3500
+  - Haplotype mapping
+  - Phylogenetic tree generation (maximum likelihood and Bayesian methods)
+  - Cell migration analysis
+  edam-topics:
+  - Population genetics
+  - Nucleic acid structure analysis
+  - Zoology
   galaxy: ''
   homepage: https://peterbeerli.com/migrate-html5/index.html
   id: MIGRATE
@@ -12994,17 +11990,12 @@
   description: A lightweight Python3 pipeline whose purpose is to facilitate the identification
     of expressed loci from RNA-Seq data and to select the best models in each locus.
   edam-operations:
-  - term: Splice transcript prediction
-    url: http://edamontology.org/operation_0264
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
-  edam-topics:
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
+  - Splice transcript prediction
+  - Gene prediction
+  - RNA-Seq analysis
+  edam-topics:
+  - RNA-seq
+  - Gene transcripts
   galaxy: ''
   homepage: https://github.com/lucventurini/mikado
   id: mikado
@@ -13100,11 +12091,9 @@
   description: Short-read assembler based on a de Bruijn graph, capable of assembling
     a human genome on a desktop computer in a day.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
+  - Genome assembly
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'Minia: Short-read assembler based on a de Bruijn graph'
     title: Minia 3.2.6
@@ -13130,13 +12119,10 @@
     It takes all-vs-all read self-mappings (typically by minimap) as input and outputs
     an assembly graph in the GFA format.
   edam-operations:
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
+  - De-novo assembly
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Genomics
+  - Sequence assembly
   galaxy:
   - description: 'miniasm: Ultrafast de novo assembly for long noisy reads'
     title: miniasm 0.3_r179+galaxy1
@@ -13182,11 +12168,9 @@
   - 2.24-gcccore-11.3.0
   description: Pairwise aligner for genomic and spliced nucleotide sequences
   edam-operations:
-  - term: Pairwise sequence alignment
-    url: http://edamontology.org/operation_0491
+  - Pairwise sequence alignment
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Mapping
   galaxy:
   - description: 'Map with minimap2: A fast pairwise aligner for genomic and spliced
       nucleotide sequences'
@@ -13216,15 +12200,11 @@
     penalty, splicing and frameshift. It is primarily intended for annotating protein-coding
     genes in a new species using known genes from other species.
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  - term: Protein sequence analysis
-    url: http://edamontology.org/operation_2479
+  - Sequence alignment
+  - Protein sequence analysis
   edam-topics:
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence sites, features and motifs
+  - Sequence analysis
   galaxy: ''
   homepage: https://github.com/lh3/miniprot
   id: miniprot
@@ -13244,19 +12224,13 @@
   - 4.9.6--1
   description: MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler
   edam-operations:
-  - term: Local alignment
-    url: http://edamontology.org/operation_0495
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - Local alignment
+  - k-mer counting
+  - Sequence assembly
+  - Read mapping
+  edam-topics:
+  - Sequence assembly
+  - RNA-Seq
   galaxy: ''
   homepage: https://sourceforge.net/p/mira-assembler/wiki/Home/
   id: mira
@@ -13299,15 +12273,11 @@
   description: miRDeep2 discovers active known or novel miRNAs from deep sequencing
     data.
   edam-operations:
-  - term: miRNA target prediction
-    url: http://edamontology.org/operation_0463
-  - term: miRNA expression analysis
-    url: http://edamontology.org/operation_3792
+  - miRNA target prediction
+  - miRNA expression analysis
   edam-topics:
-  - term: Functional, regulatory and non-coding RNA
-    url: http://edamontology.org/topic_0659
-  - term: RNA immunoprecipitation
-    url: http://edamontology.org/topic_3794
+  - Functional, regulatory and non-coding RNA
+  - RNA immunoprecipitation
   galaxy:
   - description: 'MiRDeep2: identification of novel and known miRNAs'
     title: MiRDeep2 2.0.1.2+galaxy0
@@ -13356,21 +12326,14 @@
   bunya: ''
   description: Find, circularise and annotate mitogenome from PacBio assemblies
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  - term: Sequence classification
-    url: http://edamontology.org/operation_2995
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genome assembly
+  - De-novo assembly
+  - Genome annotation
+  - Sequence classification
+  edam-topics:
+  - Sequence assembly
+  - Sequence analysis
+  - Genomics
   galaxy:
   - description: 'MitoHiFi: assembly mitogenomes from Pacbio HiFi reads'
     title: MitoHiFi 3+galaxy0
@@ -13394,13 +12357,10 @@
   bunya: ''
   description: De novo metazoan mitochondrial genome annotation.
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Genome annotation
   edam-topics:
-  - term: Zoology
-    url: http://edamontology.org/topic_3500
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
+  - Zoology
+  - Whole genome sequencing
   galaxy:
   - description: 'MITOS2: de-novo annotation of metazoan mitochondrial genomes'
     title: MITOS2 2.1.9+galaxy0
@@ -13425,11 +12385,9 @@
   description: Multi Locus Sequence Typing from an assembled genome or from a set
     of reads.
   edam-operations:
-  - term: Multilocus sequence typing
-    url: http://edamontology.org/operation_3840
+  - Multilocus sequence typing
   edam-topics:
-  - term: Immunoproteins and antigens
-    url: http://edamontology.org/topic_2830
+  - Immunoproteins and antigens
   galaxy:
   - description: 'MLST: Scans genomes against PubMLST schemes'
     title: MLST 2.22.0
@@ -13465,23 +12423,15 @@
     \ metagenomic sequence fragments in 10\u2009h on a single server to 50% sequence\
     \ identity."
   edam-operations:
-  - term: Sequence similarity search
-    url: http://edamontology.org/operation_0346
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Proteins
-    url: http://edamontology.org/topic_0078
-  - term: Nucleic acids
-    url: http://edamontology.org/topic_0077
-  - term: Gene and protein families
-    url: http://edamontology.org/topic_0623
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
+  - Sequence similarity search
+  - Sequence alignment
+  edam-topics:
+  - Metagenomics
+  - Sequence analysis
+  - Proteins
+  - Nucleic acids
+  - Gene and protein families
+  - Taxonomy
   galaxy: ''
   homepage: https://mmseqs.com
   id: mmseqs2
@@ -13525,25 +12475,16 @@
     to different genetic backgrounds. The MOB-suite is designed to be a modular set
     of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.'
   edam-operations:
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
-  - term: Plasmid map drawing
-    url: http://edamontology.org/operation_0578
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Deposition
-    url: http://edamontology.org/operation_3431
-  edam-topics:
-  - term: Mobile genetic elements
-    url: http://edamontology.org/topic_0798
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Public health and epidemiology
-    url: http://edamontology.org/topic_3305
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Biomarkers
-    url: http://edamontology.org/topic_3360
+  - Clustering
+  - Plasmid map drawing
+  - Sequence assembly
+  - Deposition
+  edam-topics:
+  - Mobile genetic elements
+  - Whole genome sequencing
+  - Public health and epidemiology
+  - Sequence assembly
+  - Biomarkers
   galaxy:
   - description: 'MOB-Recon: Type contigs and extract plasmid sequences'
     title: MOB-Recon 3.0.3+galaxy0
@@ -13633,11 +12574,9 @@
   bunya: ''
   description: A modest Feature Finder to extract features in MS1 Data.
   edam-operations:
-  - term: Protein feature detection
-    url: http://edamontology.org/operation_3092
+  - Protein feature detection
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
+  - Proteomics
   galaxy:
   - description: 'moFF: extracts MS1 intensities from spectrum files'
     title: moFF 2.0.3.0
@@ -13682,11 +12621,9 @@
   description: A proteomics search algorithm specifically designed for high-resolution
     tandem mass spectra.
   edam-operations:
-  - term: Peptide database search
-    url: http://edamontology.org/operation_3646
+  - Peptide database search
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
+  - Proteomics
   galaxy:
   - description: 'Morpheus: database search algorithm for high-resolution tandem mass
       spectra'
@@ -13712,29 +12649,18 @@
   description: Open-source, platform-independent, community-supported software for
     describing and comparing microbial communities
   edam-operations:
-  - term: DNA barcoding
-    url: http://edamontology.org/operation_3200
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Sequence clustering
-    url: http://edamontology.org/operation_0291
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Sequence read processing
-    url: http://edamontology.org/operation_3921
-  - term: Phylogenetic analysis
-    url: http://edamontology.org/operation_0324
-  edam-topics:
-  - term: Microbial ecology
-    url: http://edamontology.org/topic_3697
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
+  - DNA barcoding
+  - Sequencing quality control
+  - Sequence clustering
+  - Taxonomic classification
+  - Visualisation
+  - Sequence read processing
+  - Phylogenetic analysis
+  edam-topics:
+  - Microbial ecology
+  - Taxonomy
+  - Sequence analysis
+  - Phylogeny
   galaxy:
   - description: 'Align.check: Calculate the number of potentially misaligned bases'
     title: Align.check 1.39.5.0
@@ -14175,13 +13101,10 @@
     to save and combine results from different queries, easy integration into larger
     workflows, and a comprehensive Web Services layer.
   edam-operations:
-  - term: Query and retrieval
-    url: http://edamontology.org/operation_0224
+  - Query and retrieval
   edam-topics:
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: Genotype and phenotype
-    url: http://edamontology.org/topic_0625
+  - Model organisms
+  - Genotype and phenotype
   galaxy:
   - description: 'MouseMine: server'
     title: MouseMine 1.0.0
@@ -14207,11 +13130,9 @@
     of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC)
     methods to estimate the posterior distribution of model parameters.
   edam-operations:
-  - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
-    url: http://edamontology.org/operation_0547
+  - Phylogenetic tree generation (maximum likelihood and Bayesian methods)
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
+  - Phylogenetics
   galaxy: ''
   homepage: http://nbisweden.github.io/MrBayes/
   id: mrbayes
@@ -14247,17 +13168,12 @@
     of the MRtrix3 framework and general-purpose image processing applications provided
     with the software
   edam-operations:
-  - term: Image analysis
-    url: http://edamontology.org/operation_3443
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  edam-topics:
-  - term: MRI
-    url: http://edamontology.org/topic_3444
-  - term: Medical imaging
-    url: http://edamontology.org/topic_3384
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
+  - Image analysis
+  - Visualisation
+  edam-topics:
+  - MRI
+  - Medical imaging
+  - Data visualisation
   galaxy: ''
   homepage: https://github.com/MRtrix3/mrtrix3
   id: mrtrix
@@ -14281,15 +13197,11 @@
     companies (with vendor libraries, Windows-only). For Windows users, there is also
     a GUI, msConvertGUI.
   edam-operations:
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Filtering
+  - Formatting
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
+  - Proteomics
+  - Proteomics experiment
   galaxy:
   - description: 'msconvert: Convert and/or filter mass spectrometry files'
     title: msconvert 3.0.20287.2
@@ -14312,17 +13224,12 @@
   bunya: ''
   description: Tool for mass spectra metadata annotation.
   edam-operations:
-  - term: Annotation
-    url: http://edamontology.org/operation_0226
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
+  - Annotation
+  - Standardisation and normalisation
   edam-topics:
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
-  - term: Compound libraries and screening
-    url: http://edamontology.org/topic_3343
-  - term: Data submission, annotation and curation
-    url: http://edamontology.org/topic_0219
+  - Metabolomics
+  - Compound libraries and screening
+  - Data submission, annotation and curation
   galaxy:
   - description: 'MSMetaEnhancer: annotate MS data'
     title: MSMetaEnhancer 0.3.0+galaxy1
@@ -14345,27 +13252,17 @@
   bunya: ''
   description: Statistical tool for quantitative mass spectrometry-based proteomics.
   edam-operations:
-  - term: Statistical modelling
-    url: http://edamontology.org/operation_3664
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Differential protein expression analysis
-    url: http://edamontology.org/operation_3741
-  - term: Statistical inference
-    url: http://edamontology.org/operation_3658
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - Statistical modelling
+  - Data handling
+  - Differential protein expression analysis
+  - Statistical inference
+  - Quantification
+  - Standardisation and normalisation
+  edam-topics:
+  - Proteomics
+  - Proteomics experiment
+  - Statistics and probability
+  - Workflows
   galaxy:
   - description: 'MSstats: statistical relative protein significance analysis in DDA,
       SRM and DIA Mass Spectrometry'
@@ -14436,19 +13333,13 @@
     logs and compiles a HTML report. It's a general use tool, perfect for summarising
     the output from numerous bioinformatics tools.
   edam-operations:
-  - term: Validation
-    url: http://edamontology.org/operation_2428
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
+  - Validation
+  - Sequencing quality control
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Sequencing
+  - Bioinformatics
+  - Sequence analysis
+  - Genomics
   galaxy:
   - description: 'MultiQC: aggregate results from bioinformatics analyses into a single
       report'
@@ -14475,17 +13366,12 @@
     finished or draft sequence. Basically it is a ultra-fast alignment of large-scale
     DNA and protein sequences
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
+  - Sequence alignment
+  - Read mapping
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Genomics
+  - Mapping
+  - Sequencing
   galaxy:
   - description: 'Delta-Filter: Filters alignment (delta) file from nucmer'
     title: Delta-Filter 4.0.0rc1+galaxy3
@@ -14625,25 +13511,16 @@
     knocked-out. Alternatively, on a smaller scale transcripts of interests could
     be synthesized in-vitro'
   edam-operations:
-  - term: Post-translation modification site prediction
-    url: http://edamontology.org/operation_0417
-  - term: PolyA signal detection
-    url: http://edamontology.org/operation_0428
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
-  edam-topics:
-  - term: Functional, regulatory and non-coding RNA
-    url: http://edamontology.org/topic_0659
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
+  - Post-translation modification site prediction
+  - PolyA signal detection
+  - Genotyping
+  - k-mer counting
+  edam-topics:
+  - Functional, regulatory and non-coding RNA
+  - RNA-Seq
+  - Gene transcripts
+  - Transcriptomics
+  - Transcription factors and regulatory sites
   galaxy:
   - description: 'SampComp: to compare Nanopolished datasets'
     title: SampComp 1.0.0rc3.post2+galaxy1
@@ -14689,13 +13566,10 @@
     bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for
     long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences
   edam-operations:
-  - term: Scatter plot plotting
-    url: http://edamontology.org/operation_2940
-  - term: Box-Whisker plot plotting
-    url: http://edamontology.org/operation_2943
+  - Scatter plot plotting
+  - Box-Whisker plot plotting
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy:
   - description: 'NanoPlot: Plotting suite for Oxford Nanopore sequencing data and
       alignments'
@@ -14721,25 +13595,16 @@
   description: A package for detecting cytosine methylations and genetic variations
     from nanopore MinION sequencing data.
   edam-operations:
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Methylation analysis
-    url: http://edamontology.org/operation_3204
-  - term: Mapping
-    url: http://edamontology.org/operation_2429
-  edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
+  - Statistical calculation
+  - Genetic variation analysis
+  - Sequence assembly
+  - Methylation analysis
+  - Mapping
+  edam-topics:
+  - Sequence analysis
+  - Sequencing
+  - Genetic variation
+  - Statistics and probability
   galaxy:
   - description: 'Nanopolish variants: - Find SNPs of basecalled merged Nanopore reads
       and polishes the consensus sequences'
@@ -14817,15 +13682,11 @@
     across NCBI databases. Find and download sequence, annotation, and metadata for
     genes and genomes using our command-line tools or web interface.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Sequence database search
-    url: http://edamontology.org/operation_0338
-  - term: Data retrieval
-    url: http://edamontology.org/operation_2422
+  - Data handling
+  - Sequence database search
+  - Data retrieval
   edam-topics:
-  - term: Biological databases
-    url: http://edamontology.org/topic_3071
+  - Biological databases
   galaxy: ''
   homepage: https://www.ncbi.nlm.nih.gov/datasets/
   id: ncbi-datasets-cli
@@ -14893,8 +13754,7 @@
     regression testing scientific models or datasets in a test-driven development
     environment.
   edam-operations:
-  - term: Regression analysis
-    url: http://edamontology.org/operation_3659
+  - Regression analysis
   edam-topics: ''
   galaxy: ''
   homepage: https://gitlab.com/remikz/nccmp
@@ -14955,8 +13815,7 @@
   bunya: ''
   description: Ncview is a netCDF visual browser.
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Visualisation
   edam-topics: ''
   galaxy: ''
   homepage: https://cirrus.ucsd.edu/ncview/
@@ -15014,19 +13873,13 @@
     not require user interaction, which makes them suitable for automating phylogeny
     processing tasks.
   edam-operations:
-  - term: Phylogenetic tree generation
-    url: http://edamontology.org/operation_0323
-  - term: Phylogenetic tree analysis
-    url: http://edamontology.org/operation_0324
-  - term: Phylogenetic tree reconstruction
-    url: http://edamontology.org/operation_3478
+  - Phylogenetic tree generation
+  - Phylogenetic tree analysis
+  - Phylogenetic tree reconstruction
   edam-topics:
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Phylogeny
+  - Genomics
+  - Computer science
   galaxy:
   - description: 'Newick Display: visualize a phylogenetic tree'
     title: Newick Display 1.6+galaxy1
@@ -15074,19 +13927,13 @@
     software containers. It allows the adaptation of pipelines written in the most
     common scripting languages.
   edam-operations:
-  - term: Service composition
-    url: http://edamontology.org/operation_3762
-  - term: Service invocation
-    url: http://edamontology.org/operation_3763
-  edam-topics:
-  - term: Software engineering
-    url: http://edamontology.org/topic_3372
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Service composition
+  - Service invocation
+  edam-topics:
+  - Software engineering
+  - Workflows
+  - Bioinformatics
+  - Genomics
   galaxy: ''
   homepage: https://www.nextflow.io/
   id: nextflow
@@ -15120,19 +13967,13 @@
     sequencing (TGS) long reads with approximately 15-10% sequencing errors, please
     use NextDenovo'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Plant biology
-    url: http://edamontology.org/topic_0780
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Genome assembly
+  - Scaffolding
+  - k-mer counting
+  edam-topics:
+  - Sequence assembly
+  - Plant biology
+  - Mapping
   galaxy: ''
   homepage: https://github.com/Nextomics/NextPolish
   id: nextpolish
@@ -15191,21 +14032,14 @@
   description: NGSUtils is a suite of software tools for working with next-generation
     sequencing datasets
   edam-operations:
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  - term: Sequence contamination filtering
-    url: http://edamontology.org/operation_3187
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - Read pre-processing
+  - Sequencing quality control
+  - Variant calling
+  - Formatting
+  - Sequence contamination filtering
+  edam-topics:
+  - Genomics
+  - Transcriptomics
   galaxy:
   - description: 'BAM filter: Removes reads from a BAM file based on criteria'
     title: BAM filter 0.5.9
@@ -15232,8 +14066,7 @@
   description: Nearly Infinite Neighbor Joining Application
   edam-operations: ''
   edam-topics:
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
+  - Phylogeny
   galaxy: ''
   homepage: https://github.com/TravisWheelerLab/NINJA
   id: ninja
@@ -15315,15 +14148,11 @@
     files. They were mainly designed to help us for analyzing Next Generation Sequencer
     outputs (454 or Illumina) in the context of DNA Metabarcoding.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
+  - Sequence analysis
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Sequence analysis
+  - DNA
+  - Sequencing
   galaxy:
   - description: 'obiannotate: Adds/Edits sequence record annotations'
     title: obiannotate 1.2.13
@@ -15399,61 +14228,34 @@
     Raw and intermediate mass spectrometry data can be visualised with the included
     viewer TOPPView.
   edam-operations:
-  - term: Protein identification
-    url: http://edamontology.org/operation_3767
-  - term: Parsing
-    url: http://edamontology.org/operation_1812
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Chromatographic alignment
-    url: http://edamontology.org/operation_3628
-  - term: Mass spectra calibration
-    url: http://edamontology.org/operation_3627
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  - term: Protein quantification
-    url: http://edamontology.org/operation_3630
-  - term: Retention time prediction
-    url: http://edamontology.org/operation_3633
-  - term: Annotation
-    url: http://edamontology.org/operation_0226
-  - term: Protein feature detection
-    url: http://edamontology.org/operation_3092
-  - term: Isotope-coded protein label
-    url: http://edamontology.org/operation_3705
-  - term: Label-free quantification
-    url: http://edamontology.org/operation_3634
-  - term: iTRAQ
-    url: http://edamontology.org/operation_3639
-  - term: Peptide identification
-    url: http://edamontology.org/operation_3631
-  - term: Peak detection
-    url: http://edamontology.org/operation_3215
-  - term: Mass spectrum visualisation
-    url: http://edamontology.org/operation_3694
-  - term: Labeled quantification
-    url: http://edamontology.org/operation_3635
-  - term: Splitting
-    url: http://edamontology.org/operation_3359
-  - term: Spectral analysis
-    url: http://edamontology.org/operation_3214
-  - term: Deisotoping
-    url: http://edamontology.org/operation_3629
-  - term: Target-Decoy
-    url: http://edamontology.org/operation_3649
-  - term: Prediction and recognition (protein)
-    url: http://edamontology.org/operation_3023
-  - term: Comparison
-    url: http://edamontology.org/operation_2424
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  edam-topics:
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Protein identification
+  - Parsing
+  - Data handling
+  - Chromatographic alignment
+  - Mass spectra calibration
+  - Formatting
+  - Protein quantification
+  - Retention time prediction
+  - Annotation
+  - Protein feature detection
+  - Isotope-coded protein label
+  - Label-free quantification
+  - iTRAQ
+  - Peptide identification
+  - Peak detection
+  - Mass spectrum visualisation
+  - Labeled quantification
+  - Splitting
+  - Spectral analysis
+  - Deisotoping
+  - Target-Decoy
+  - Prediction and recognition (protein)
+  - Comparison
+  - Standardisation and normalisation
+  edam-topics:
+  - Proteomics experiment
+  - Proteomics
+  - Metabolomics
   galaxy:
   - description: 'XTandemAdapter: Annotates MS/MS spectra using X! Tandem.'
     title: XTandemAdapter 2.8+galaxy0
@@ -15630,25 +14432,16 @@
     gene duplication events from the gene trees to branches in the species tree. OrthoFinder
     also provides comprehensive statistics for comparative genomic analyses.
   edam-operations:
-  - term: Genome comparison
-    url: http://edamontology.org/operation_3209
-  - term: Phylogenetic tree generation (from molecular sequences)
-    url: http://edamontology.org/operation_0540
-  - term: Phylogenetic tree analysis
-    url: http://edamontology.org/operation_0324
-  - term: Genome alignment
-    url: http://edamontology.org/operation_3182
-  edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Phylogenomics
-    url: http://edamontology.org/topic_0194
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
-  - term: Comparative genomics
-    url: http://edamontology.org/topic_0797
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Genome comparison
+  - Phylogenetic tree generation (from molecular sequences)
+  - Phylogenetic tree analysis
+  - Genome alignment
+  edam-topics:
+  - Phylogenetics
+  - Phylogenomics
+  - Bioinformatics
+  - Comparative genomics
+  - Sequence analysis
   galaxy:
   - description: 'OrthoFinder: finds orthogroups in a set of proteomes'
     title: OrthoFinder 2.5.5+galaxy0
@@ -15734,27 +14527,17 @@
     variant, and return a file of the same format. Pangolin's models can also be used
     with custom sequences.
   edam-operations:
-  - term: Splice site prediction
-    url: http://edamontology.org/operation_0433
-  - term: Sequence merging
-    url: http://edamontology.org/operation_0232
-  - term: Alternative splicing prediction
-    url: http://edamontology.org/operation_0264
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Variant classification
-    url: http://edamontology.org/operation_3225
-  edam-topics:
-  - term: RNA splicing
-    url: http://edamontology.org/topic_3320
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Exome sequencing
-    url: http://edamontology.org/topic_3676
+  - Splice site prediction
+  - Sequence merging
+  - Alternative splicing prediction
+  - Genotyping
+  - Variant classification
+  edam-topics:
+  - RNA splicing
+  - Genetic variation
+  - Gene transcripts
+  - RNA-Seq
+  - Exome sequencing
   galaxy:
   - description: 'Pangolin: Phylogenetic Assignment of Outbreak Lineages'
     title: Pangolin 4.3+galaxy2
@@ -15802,13 +14585,10 @@
     \ be done interactively in 3D or programmatically using ParaView\u2019s batch\
     \ processing capabilities."
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Visualisation
   edam-topics:
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
-  - term: Imaging
-    url: http://edamontology.org/topic_3382
+  - Data visualisation
+  - Imaging
   galaxy: ''
   homepage: https://www.paraview.org/
   id: paraview
@@ -15861,17 +14641,12 @@
     and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible
     platform for visualizing genome alignments and phylogenetic trees.
   edam-operations:
-  - term: SNP detection
-    url: http://edamontology.org/operation_0484
-  - term: Genome alignment
-    url: http://edamontology.org/operation_3182
-  edam-topics:
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Structure analysis
-    url: http://edamontology.org/topic_0081
+  - SNP detection
+  - Genome alignment
+  edam-topics:
+  - DNA polymorphism
+  - Phylogenetics
+  - Structure analysis
   galaxy: ''
   homepage: https://github.com/marbl/parsnp
   id: parsnp
@@ -15894,17 +14669,12 @@
     with pathway and gene set (enrichment) analysis tools for large-scale and fully
     automated analysis.
   edam-operations:
-  - term: Pathway or network analysis
-    url: http://edamontology.org/operation_2497
-  - term: Pathway or network visualisation
-    url: http://edamontology.org/operation_3083
+  - Pathway or network analysis
+  - Pathway or network visualisation
   edam-topics:
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
-  - term: Systems biology
-    url: http://edamontology.org/topic_2259
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
+  - Molecular interactions, pathways and networks
+  - Systems biology
+  - Data visualisation
   galaxy:
   - description: 'Pathview: for pathway based data integration and visualization'
     title: Pathview 1.34.0+galaxy0
@@ -15933,15 +14703,11 @@
     display and transform results from the Kraken and Centrifuge classifiers using
     interactive tables, heatmaps and flow diagrams.
   edam-operations:
-  - term: Annotation
-    url: http://edamontology.org/operation_0226
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
+  - Annotation
+  - Taxonomic classification
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
+  - Metagenomics
+  - Model organisms
   galaxy:
   - description: 'Pavian: Interactive analysis of metagenomics data'
     title: Pavian 1.0
@@ -15964,17 +14730,12 @@
   bunya: ''
   description: Multithread blat algorithm speeding up aligning sequences to genomes.
   edam-operations:
-  - term: Protein threading
-    url: http://edamontology.org/operation_0302
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
-  edam-topics:
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
+  - Protein threading
+  - Read mapping
+  edam-topics:
+  - RNA-seq
+  - Mapping
+  - Gene transcripts
   galaxy: ''
   homepage: https://github.com/icebert/pblat
   id: pblat
@@ -15997,25 +14758,16 @@
   description: Productive visualization of high-throughput sequencing data using the
     SeqCode open portable platform.
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Peak calling
-    url: http://edamontology.org/operation_3222
-  - term: Essential dynamics
-    url: http://edamontology.org/operation_3891
-  - term: Phylogenetic footprinting
-    url: http://edamontology.org/operation_0327
-  edam-topics:
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Epigenetics
-    url: http://edamontology.org/topic_3295
-  - term: Methylated DNA immunoprecipitation
-    url: http://edamontology.org/topic_3674
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
+  - Visualisation
+  - Peak calling
+  - Essential dynamics
+  - Phylogenetic footprinting
+  edam-topics:
+  - ChIP-seq
+  - RNA-Seq
+  - Epigenetics
+  - Methylated DNA immunoprecipitation
+  - Transcription factors and regulatory sites
   galaxy:
   - description: 'Paired-end histogram: of insert size frequency'
     title: Paired-end histogram 1.0.1
@@ -16042,11 +14794,9 @@
     overlaps without requiring the target fragment size as input. In addition, it
     implements a statistical test for minimizing false-positive results.
   edam-operations:
-  - term: Sequence merging
-    url: http://edamontology.org/operation_0232
+  - Sequence merging
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'Pear: Paired-End read merger'
     title: Pear 0.9.6.2
@@ -16095,27 +14845,17 @@
     PTM localization scores and redoing the protein inference, PeptideShaker attempts
     to give you the best possible understanding of your proteomics data
   edam-operations:
-  - term: PTM localisation
-    url: http://edamontology.org/operation_3755
-  - term: Protein identification
-    url: http://edamontology.org/operation_3767
-  - term: Structure visualisation
-    url: http://edamontology.org/operation_0570
-  - term: Validation
-    url: http://edamontology.org/operation_2428
-  - term: Peptide identification
-    url: http://edamontology.org/operation_3631
-  - term: Mass spectrum visualisation
-    url: http://edamontology.org/operation_3694
-  - term: Enrichment analysis
-    url: http://edamontology.org/operation_3501
-  edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Proteome
-    url: http://edamontology.org/topic_0644
+  - PTM localisation
+  - Protein identification
+  - Structure visualisation
+  - Validation
+  - Peptide identification
+  - Mass spectrum visualisation
+  - Enrichment analysis
+  edam-topics:
+  - Proteomics
+  - Proteomics experiment
+  - Proteome
   galaxy:
   - description: 'FastaCLI: Appends decoy sequences to FASTA files'
     title: FastaCLI 4.0.41+galaxy1
@@ -16173,27 +14913,17 @@
   bunya: ''
   description: Semi-supervised learning for peptide identification from MS/MS data.
   edam-operations:
-  - term: Protein fragment weight comparison
-    url: http://edamontology.org/operation_2929
-  - term: Protein identification
-    url: http://edamontology.org/operation_3767
-  - term: Blind peptide database search
-    url: http://edamontology.org/operation_3647
-  - term: Peptide identification
-    url: http://edamontology.org/operation_3631
-  - term: Target-Decoy
-    url: http://edamontology.org/operation_3649
-  - term: Validation of peptide-spectrum matches
-    url: http://edamontology.org/operation_3648
-  edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
+  - Protein fragment weight comparison
+  - Protein identification
+  - Blind peptide database search
+  - Peptide identification
+  - Target-Decoy
+  - Validation of peptide-spectrum matches
+  edam-topics:
+  - Proteomics
+  - Proteomics experiment
+  - Statistics and probability
+  - Machine learning
   galaxy:
   - description: 'Search engine output to Pin converter: to create Percolator input
       files'
@@ -16247,11 +14977,9 @@
   description: This tool is used to search a FASTA sequence against a library of Pfam
     HMM.
   edam-operations:
-  - term: Protein sequence analysis
-    url: http://edamontology.org/operation_2479
+  - Protein sequence analysis
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'PfamScan: search a FASTA sequence against a library of Pfam HMM'
     title: PfamScan 1.6+galaxy0
@@ -16273,25 +15001,16 @@
   description: Pharokka is a rapid standardised annotation tool for bacteriophage
     genomes and metagenomes.
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  - term: Antimicrobial resistance prediction
-    url: http://edamontology.org/operation_3482
-  - term: tRNA gene prediction
-    url: http://edamontology.org/operation_0464
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Functional, regulatory and non-coding RNA
-    url: http://edamontology.org/topic_0659
+  - Genome annotation
+  - Antimicrobial resistance prediction
+  - tRNA gene prediction
+  - Formatting
+  - Sequence assembly
+  edam-topics:
+  - Metagenomics
+  - Sequence sites, features and motifs
+  - Workflows
+  - Functional, regulatory and non-coding RNA
   galaxy:
   - description: 'pharokka: Rapid standardised annotation tool for bacteriophage genomes
       and metagenomes'
@@ -16356,19 +15075,13 @@
   description: Provides a set of classes and tools to facilitate the import, storage,
     analysis, and graphical display of microbiome census data.
   edam-operations:
-  - term: Deposition
-    url: http://edamontology.org/operation_3431
-  - term: Analysis
-    url: http://edamontology.org/operation_2945
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Deposition
+  - Analysis
+  - Visualisation
   edam-topics:
-  - term: Microbiology
-    url: http://edamontology.org/topic_3301
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Microbiology
+  - Sequence analysis
+  - Metagenomics
   galaxy:
   - description: 'Phyloseq Biom Filtering: biom file filter'
     title: Phyloseq Biom Filtering 1.22.3.2
@@ -16395,15 +15108,11 @@
   bunya: ''
   description: Phylogenetic estimation software using Maximum Likelihood
   edam-operations:
-  - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
-    url: http://edamontology.org/operation_0547
+  - Phylogenetic tree generation (maximum likelihood and Bayesian methods)
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
+  - Phylogenetics
+  - Bioinformatics
+  - Phylogenetics
   galaxy:
   - description: 'PhyML: Phylogeny software based on the maximum-likelihood method'
     title: PhyML 3.3.20220408+galaxy0
@@ -16437,13 +15146,10 @@
     (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone
     program or within the GATK4 program.
   edam-operations:
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
+  - Genetic variation analysis
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Sequencing
+  - Data management
   galaxy:
   - description: 'FixMateInformation: ensure that all mate-pair information is in
       sync between each read and it''s mate pair'
@@ -16575,23 +15281,15 @@
     metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full
     genomes.
   edam-operations:
-  - term: Phylogenetic reconstruction
-    url: http://edamontology.org/operation_3478
-  - term: Expression analysis
-    url: http://edamontology.org/operation_2495
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  - term: DNA barcoding
-    url: http://edamontology.org/operation_3200
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Microbial ecology
-    url: http://edamontology.org/topic_3697
-  - term: Functional, regulatory and non-coding RNA
-    url: http://edamontology.org/topic_0659
-  - term: Metagenomic sequencing
-    url: http://edamontology.org/topic_3837
+  - Phylogenetic reconstruction
+  - Expression analysis
+  - Genome annotation
+  - DNA barcoding
+  edam-topics:
+  - Metagenomics
+  - Microbial ecology
+  - Functional, regulatory and non-coding RNA
+  - Metagenomic sequencing
   galaxy:
   - description: 'Categorize: by collapsing hierarchical data to a specified functional
       level'
@@ -16636,23 +15334,15 @@
     of Unobserved States) is a software for predicting functional abundances based
     only on marker gene sequences.
   edam-operations:
-  - term: Phylogenetic reconstruction
-    url: http://edamontology.org/operation_3478
-  - term: Expression analysis
-    url: http://edamontology.org/operation_2495
-  - term: Rarefaction
-    url: http://edamontology.org/operation_3797
-  - term: Pathway analysis
-    url: http://edamontology.org/operation_3928
-  edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Microbiology
-    url: http://edamontology.org/topic_3301
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Metagenomic sequencing
-    url: http://edamontology.org/topic_3837
+  - Phylogenetic reconstruction
+  - Expression analysis
+  - Rarefaction
+  - Pathway analysis
+  edam-topics:
+  - Metagenomics
+  - Microbiology
+  - Phylogenetics
+  - Metagenomic sequencing
   galaxy:
   - description: 'PICRUSt2 Add descriptions: column to a function abundance table'
     title: PICRUSt2 Add descriptions 2.5.1+galaxy0
@@ -16738,11 +15428,9 @@
   description: Read alignment analysis to diagnose, report, and automatically improve
     de novo genome assemblies.
   edam-operations:
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
+  - Sequence assembly
   edam-topics:
-  - term: Assembly
-    url: http://edamontology.org/topic_0196
+  - Assembly
   galaxy:
   - description: 'pilon: An automated genome assembly improvement and variant detection
       tool'
@@ -16776,25 +15464,16 @@
     analysis in a simple to use, transparent, accessible, reproducible, and user-friendly
     environment'
   edam-operations:
-  - term: Essential dynamics
-    url: http://edamontology.org/operation_3891
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  - term: Imputation
-    url: http://edamontology.org/operation_3557
-  - term: Parsing
-    url: http://edamontology.org/operation_1812
-  edam-topics:
-  - term: PCR experiment
-    url: http://edamontology.org/topic_3519
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: Biomarkers
-    url: http://edamontology.org/topic_3360
-  - term: Microarray experiment
-    url: http://edamontology.org/topic_3518
+  - Essential dynamics
+  - Quantification
+  - Standardisation and normalisation
+  - Imputation
+  - Parsing
+  edam-topics:
+  - PCR experiment
+  - Transcriptomics
+  - Biomarkers
+  - Microarray experiment
   galaxy:
   - description: 'PIPE-T: A tool for analyzing RTqPCR expression data'
     title: PIPE-T 1.0
@@ -16841,11 +15520,9 @@
     to perform a range of basic, large-scale analyses in a computationally efficient
     manner.
   edam-operations:
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
+  - Genetic variation analysis
   edam-topics:
-  - term: GWAS study
-    url: http://edamontology.org/topic_3517
+  - GWAS study
   galaxy: ''
   homepage: http://zzz.bwh.harvard.edu/plink/
   id: plink
@@ -16895,11 +15572,9 @@
   bunya: ''
   description: 'PnetCDF: A Parallel I/O Library for NetCDF File Access'
   edam-operations:
-  - term: Aggregation
-    url: http://edamontology.org/operation_3436
+  - Aggregation
   edam-topics:
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Computer science
   galaxy: ''
   homepage: https://parallel-netcdf.github.io/
   id: pnetcdf
@@ -16963,13 +15638,10 @@
   description: Flexible toolkit for exploring datasets generated by nanopore sequencing
     devices from MinION for the purposes of quality control and downstream analysis.
   edam-operations:
-  - term: Nucleic acid sequence analysis
-    url: http://edamontology.org/operation_2478
+  - Nucleic acid sequence analysis
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - DNA
+  - Sequencing
   galaxy:
   - description: 'Extract nanopore events: from a set of sequencing reads'
     title: Extract nanopore events 0.6.1a1.1
@@ -17031,11 +15703,9 @@
   description: Tools for performing taxonomic assignment based on phylogeny using
     pplacer and clst.
   edam-operations:
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
+  - Taxonomic classification
   edam-topics:
-  - term: Taxonomy
-    url: http://edamontology.org/topic_0637
+  - Taxonomy
   galaxy: ''
   homepage: http://bioconductor.org/packages/release/bioc/html/clstutils.html
   id: pplacer
@@ -17076,11 +15746,9 @@
   bunya: ''
   description: Pretext is an OpenGL-powered pretext contact map viewer.
   edam-operations:
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
+  - Scaffolding
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Mapping
   galaxy:
   - description: 'Pretext Snapshot: image generator for Pretext contact maps'
     title: Pretext Snapshot 0.0.3+galaxy2
@@ -17109,15 +15777,11 @@
     position is found, it is accepted, and the predictions are changed for the outlying
     genes.
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
+  - Gene prediction
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Nucleic acid sites, features and motifs
-    url: http://edamontology.org/topic_3511
+  - DNA
+  - Sequence analysis
+  - Nucleic acid sites, features and motifs
   galaxy: ''
   homepage: https://code.google.com/p/gmv/
   id: prodigal
@@ -17143,11 +15807,9 @@
     implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData,
     mzXML, and mzML) and generates the peak table.
   edam-operations:
-  - term: Peak calling
-    url: http://edamontology.org/operation_3222
+  - Peak calling
   edam-topics:
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Metabolomics
   galaxy:
   - description: 'proFIA: Preprocessing of FIA-HRMS data'
     title: proFIA 3.1.0
@@ -17192,19 +15854,13 @@
   description: Software tool to annotate bacterial, archaeal and viral genomes quickly
     and produce standards-compliant output files.
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
-  - term: Coding region prediction
-    url: http://edamontology.org/operation_0436
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Gene prediction
+  - Coding region prediction
+  - Genome annotation
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: Virology
-    url: http://edamontology.org/topic_0781
+  - Genomics
+  - Model organisms
+  - Virology
   galaxy:
   - description: 'Prokka: Prokaryotic genome annotation'
     title: Prokka 1.14.6+galaxy1
@@ -17275,15 +15931,11 @@
     recommend our users to do so, because assemblers may produce overrepresented seqeuences.
     In such a case, The final step 4 can be applied to remove those seqeuences'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Read binning
-    url: http://edamontology.org/operation_3798
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
+  - Genome assembly
+  - Read binning
+  - Scaffolding
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'Purge overlaps: and haplotigs in an assembly based on read depth
       (purge_dups)'
@@ -17329,17 +15981,12 @@
   description: PycoQC computes metrics and generates interactive QC plots for Oxford
     Nanopore technologies sequencing data.
   edam-operations:
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
+  - Sequencing quality control
+  - Statistical calculation
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Data quality management
-    url: http://edamontology.org/topic_3572
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Sequence analysis
+  - Data quality management
+  - Sequencing
   galaxy:
   - description: 'Pycoqc: quality control for Nanopore sequencing data'
     title: Pycoqc 2.5.2+galaxy0
@@ -17367,17 +16014,12 @@
     pyGenomeTracks aims to produce high-quality genome browser tracks that are highly
     customizable. Currently, it is possible to plot:.'
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Visualisation
+  - Formatting
   edam-topics:
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: Imaging
-    url: http://edamontology.org/topic_3382
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - Model organisms
+  - Imaging
+  - Workflows
   galaxy:
   - description: 'pyGenomeTracks: plot genomic data tracks'
     title: pyGenomeTracks 3.8+galaxy2
@@ -17433,15 +16075,11 @@
   - 0.19.1-gcc-11.3.0                   (D)
   description: A Python module for reading and manipulating SAM/BAM/VCF/BCF files.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Sequence file editing
-    url: http://edamontology.org/operation_2121
+  - Data handling
+  - Sequence file editing
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Sequencing
+  - Mapping
   galaxy: ''
   homepage: https://github.com/pysam-developers/pysam
   id: pysam
@@ -17463,10 +16101,8 @@
     and CPUs.
   edam-operations: ''
   edam-topics:
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Machine learning
+  - Computer science
   galaxy: ''
   homepage: https://pytorch.org/
   id: pytorch
@@ -17491,23 +16127,15 @@
   description: "QIIME 2\u2122 is a next-generation microbiome bioinformatics platform\
     \ that is extensible, free, open source, and community developed."
   edam-operations:
-  - term: Demultiplexing
-    url: http://edamontology.org/operation_3933
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Taxonomic classification
-    url: http://edamontology.org/operation_3460
-  - term: Phylogenetic analysis
-    url: http://edamontology.org/operation_0324
-  edam-topics:
-  - term: Microbial ecology
-    url: http://edamontology.org/topic_3697
-  - term: Phylogeny
-    url: http://edamontology.org/topic_0084
-  - term: Metatranscriptomics
-    url: http://edamontology.org/topic_3941
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Demultiplexing
+  - Visualisation
+  - Taxonomic classification
+  - Phylogenetic analysis
+  edam-topics:
+  - Microbial ecology
+  - Phylogeny
+  - Metatranscriptomics
+  - Metagenomics
   galaxy:
   - description: 'qiime2 tools import: Import data into a QIIME 2 artifact'
     title: qiime2 tools import 2023.5.0+dist.h193f7cc9.3
@@ -18130,11 +16758,9 @@
     both a Graphical User Inteface (GUI) and a command-line interface to facilitate
     the quality control of alignment sequencing data.
   edam-operations:
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
+  - Sequencing quality control
   edam-topics:
-  - term: Data quality management
-    url: http://edamontology.org/topic_3572
+  - Data quality management
   galaxy:
   - description: 'QualiMap BamQC: '
     title: QualiMap BamQC 2.2.2d+galaxy3
@@ -18175,19 +16801,13 @@
     and file specifications are available at: https: phac-nml.github.io quasitools
     Contact gary.vandomselaar@canada.ca'
   edam-operations:
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Base-calling
-    url: http://edamontology.org/operation_3185
+  - Sequence trimming
+  - Genotyping
+  - Base-calling
   edam-topics:
-  - term: Virology
-    url: http://edamontology.org/topic_0781
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Virology
+  - Small molecules
+  - Sequencing
   galaxy:
   - description: 'Consensus Sequence: Generate a consensus sequence from a BAM file'
     title: Consensus Sequence 0.7.0+galaxy1
@@ -18249,13 +16869,10 @@
   description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
     \ of genome assemblies by computing various metrics and providing nice reports."
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Sequence assembly validation
-    url: http://edamontology.org/operation_3180
+  - Visualisation
+  - Sequence assembly validation
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'Quast: Genome assembly Quality'
     title: Quast 5.2.0+galaxy1
@@ -18284,19 +16901,13 @@
     further process to generate tabular outputs containing desired information and
     formatting.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Parsing
-    url: http://edamontology.org/operation_1812
-  - term: Query and retrieval
-    url: http://edamontology.org/operation_0224
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
+  - Data handling
+  - Parsing
+  - Query and retrieval
+  - Filtering
   edam-topics:
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - Bioinformatics
+  - Workflows
   galaxy:
   - description: 'Query Tabular: using sqlite sql'
     title: Query Tabular 3.3.1
@@ -18322,19 +16933,13 @@
   - 4.2.1-foss-2022a                        (D)
   description: Free software environment for statistical computing and graphics.
   edam-operations:
-  - term: Analysis
-    url: http://edamontology.org/operation_2945
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  edam-topics:
-  - term: Mathematics
-    url: http://edamontology.org/topic_3315
-  - term: Data architecture, analysis and design
-    url: http://edamontology.org/topic_3365
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
+  - Analysis
+  - Data handling
+  - Visualisation
+  edam-topics:
+  - Mathematics
+  - Data architecture, analysis and design
+  - Statistics and probability
   galaxy: ''
   homepage: http://www.r-project.org/
   id: r
@@ -18406,15 +17011,11 @@
     methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore
     Technologies.'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Mapping assembly
-    url: http://edamontology.org/operation_0523
+  - Genome assembly
+  - Mapping assembly
   edam-topics:
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Whole genome sequencing
+  - Sequence assembly
   galaxy:
   - description: 'Racon: Consensus module for raw de novo DNA assembly of long uncorrected
       reads'
@@ -18441,17 +17042,12 @@
   description: A feature clustering algorithm for non-targeted mass spectrometric
     metabolomics data.
   edam-operations:
-  - term: Imputation
-    url: http://edamontology.org/operation_3557
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
-  - term: Correlation
-    url: http://edamontology.org/operation_3465
+  - Imputation
+  - Standardisation and normalisation
+  - Clustering
+  - Correlation
   edam-topics:
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Metabolomics
   galaxy:
   - description: 'RAMClustR define experiment: Definition of experimental design used
       for record keeping and writing spectra data.'
@@ -18485,23 +17081,15 @@
     \ for erroneous long reads based on compacted and colored de Bruijn graphs built\
     \ from accurate short reads."
   edam-operations:
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Sequencing error detection
-    url: http://edamontology.org/operation_3195
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: Phasing
-    url: http://edamontology.org/operation_3454
-  - term: Read binning
-    url: http://edamontology.org/operation_3798
-  edam-topics:
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
+  - De-novo assembly
+  - Sequencing error detection
+  - Variant calling
+  - Phasing
+  - Read binning
+  edam-topics:
+  - DNA polymorphism
+  - Sequence assembly
+  - Whole genome sequencing
   galaxy: ''
   homepage: https://github.com/DecodeGenetics/Ratatosk
   id: ratatosk
@@ -18545,19 +17133,13 @@
 
     Raven is a de novo genome assembler for long uncorrected reads.'
   edam-operations:
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
+  - De-novo assembly
+  - Genome assembly
+  - Read pre-processing
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Sequence assembly
+  - Whole genome sequencing
+  - Genomics
   galaxy:
   - description: 'Raven: De novo assembly of Oxford Nanopore Technologies data'
     title: Raven 1.8.3+galaxy0
@@ -18581,13 +17163,10 @@
   description: A standalone tool for extracting data directly from raw files generated
     by Thermo Orbitrap family instruments.
   edam-operations:
-  - term: Parsing
-    url: http://edamontology.org/operation_1812
+  - Parsing
   edam-topics:
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
+  - Proteomics experiment
+  - Proteomics
   galaxy:
   - description: 'Raw Tools: Perform scan data parsing, quantification and quality
       control analysis of Thermo Orbitrap raw mass spectrometer files.'
@@ -18613,15 +17192,11 @@
   - 8.2.12
   description: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
-  - term: Phylogenetic tree analysis
-    url: http://edamontology.org/operation_0324
+  - Sequence analysis
+  - Phylogenetic tree analysis
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Phylogenetics
+  - Sequence analysis
   galaxy:
   - description: 'RAxML: Maximum Likelihood based inference of large phylogenetic
       trees'
@@ -18648,19 +17223,13 @@
   description: RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based
     Coordinate Generation for Open Babel.
   edam-operations:
-  - term: Nucleic acid structure prediction
-    url: http://edamontology.org/operation_0475
-  - term: Molecular dynamics
-    url: http://edamontology.org/operation_2476
-  - term: Protein geometry validation
-    url: http://edamontology.org/operation_1844
+  - Nucleic acid structure prediction
+  - Molecular dynamics
+  - Protein geometry validation
   edam-topics:
-  - term: Cheminformatics
-    url: http://edamontology.org/topic_2258
-  - term: Medicinal chemistry
-    url: http://edamontology.org/topic_0209
-  - term: Molecular biology
-    url: http://edamontology.org/topic_3047
+  - Cheminformatics
+  - Medicinal chemistry
+  - Molecular biology
   galaxy:
   - description: 'Enumerate changes: calculated with Dimorphite DL and RDKit'
     title: Enumerate changes 2020.03.4+galaxy0
@@ -18709,21 +17278,14 @@
   description: Tool for calculating the probability of nucleosome formation along
     a DNA sequence input by the user.
   edam-operations:
-  - term: Nucleosome formation or exclusion sequence prediction
-    url: http://edamontology.org/operation_0432
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: DNA binding sites
-    url: http://edamontology.org/topic_3125
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
-  - term: DNA packaging
-    url: http://edamontology.org/topic_3176
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
+  - Nucleosome formation or exclusion sequence prediction
+  - Formatting
+  edam-topics:
+  - DNA
+  - DNA binding sites
+  - Statistics and probability
+  - DNA packaging
+  - Transcription factors and regulatory sites
   galaxy: ''
   homepage: http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/
   id: recon
@@ -18747,19 +17309,13 @@
     correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect
     screening.
   edam-operations:
-  - term: Chromatographic alignment
-    url: http://edamontology.org/operation_3628
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Peak detection
-    url: http://edamontology.org/operation_3215
-  - term: Feature extraction
-    url: http://edamontology.org/operation_3937
-  - term: Alignment
-    url: http://edamontology.org/operation_2928
+  - Chromatographic alignment
+  - Quantification
+  - Peak detection
+  - Feature extraction
+  - Alignment
   edam-topics:
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Metabolomics
   galaxy:
   - description: 'recetox-aplcms - align features: align peaks across samples'
     title: recetox-aplcms - align features 0.12.0+galaxy1
@@ -18809,15 +17365,11 @@
   description: This is a program to detect and visualize RNA editing events at genomic
     scale using next-generation sequencing data.
   edam-operations:
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
+  - RNA-Seq analysis
   edam-topics:
-  - term: RNA
-    url: http://edamontology.org/topic_0099
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
+  - RNA
+  - Sequencing
+  - Data visualisation
   galaxy:
   - description: 'Red: repeat masking'
     title: Red 2018.09.10+galaxy1
@@ -18865,13 +17417,10 @@
     of the query sequence in which all the annotated repeats have been masked (default:
     replaced by Ns).'
   edam-operations:
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
+  - Genome annotation
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequence composition, complexity and repeats
-    url: http://edamontology.org/topic_0157
+  - Sequence analysis
+  - Sequence composition, complexity and repeats
   galaxy:
   - description: 'RepeatMasker: screen DNA sequences for interspersed repeats and
       low complexity regions'
@@ -18900,23 +17449,15 @@
     computational methods for identifying repeat element boundaries and family relationships
     from sequence data.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: de Novo sequencing
-    url: http://edamontology.org/operation_3644
-  - term: Genome annotation
-    url: http://edamontology.org/operation_0362
-  edam-topics:
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: Sequence composition, complexity and repeats
-    url: http://edamontology.org/topic_0157
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Mobile genetic elements
-    url: http://edamontology.org/topic_0798
+  - Genome assembly
+  - de Novo sequencing
+  - Genome annotation
+  edam-topics:
+  - Model organisms
+  - Sequence composition, complexity and repeats
+  - Whole genome sequencing
+  - Sequence assembly
+  - Mobile genetic elements
   galaxy:
   - description: 'RepeatModeler: Model repetitive DNA'
     title: RepeatModeler 2.0.4+galaxy1
@@ -18942,11 +17483,9 @@
   bunya: ''
   description: RepeatScout is a tool to discover repetitive substrings in DNA.
   edam-operations:
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
+  - k-mer counting
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
+  - DNA
   galaxy: ''
   homepage: http://bix.ucsd.edu/repeatscout/
   id: repeatscout
@@ -19015,8 +17554,7 @@
     from the posterior distribution of the parameters.'
   edam-operations: ''
   edam-topics:
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
+  - Statistics and probability
   galaxy: ''
   homepage: https://cran.r-project.org/package=rjags
   id: rjags
@@ -19038,11 +17576,9 @@
     cleanup, automated retrieval of compound information from Internet databases,
     and export to MassBank records.
   edam-operations:
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
+  - Clustering
   edam-topics:
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Metabolomics
   galaxy:
   - description: 'RMassBank: '
     title: RMassBank 3.0.0+galaxy2
@@ -19087,11 +17623,9 @@
     program. The primary difference between this distribution and the NCBI distribution
     is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
+  - Sequence analysis
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy: ''
   homepage: http://www.repeatmasker.org/RMBlast.html
   id: rmblast
@@ -19138,15 +17672,11 @@
     assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates
     the pan genome.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
+  - Genome assembly
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - DNA
+  - Genomics
+  - Mapping
   galaxy:
   - description: 'Roary: the pangenome pipeline - Quickly generate a core gene alignment
       from gff3 files'
@@ -19198,11 +17728,9 @@
     uncertainty with a statistical model and the estimation of gene expression levels
     as the sum of isoform expression levels.
   edam-operations:
-  - term: RNA-Seq quantification
-    url: http://edamontology.org/operation_3800
+  - RNA-Seq quantification
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - RNA-Seq
   galaxy: ''
   homepage: http://deweylab.github.io/RSEM/
   id: rsem
@@ -19226,11 +17754,9 @@
     RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution,
     coverage uniformity, strand specificity, transcript level RNA integrity etc.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Sequencing
   galaxy:
   - description: 'Gene Body Coverage (Bigwig): read coverage over gene body'
     title: Gene Body Coverage (Bigwig) 5.0.1+galaxy2
@@ -19331,17 +17857,12 @@
   bunya: ''
   description: Integrated development environment (IDE) for the R programming language.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Data handling
+  - Visualisation
   edam-topics:
-  - term: Mathematics
-    url: http://edamontology.org/topic_3315
-  - term: Data architecture, analysis and design
-    url: http://edamontology.org/topic_3365
-  - term: Statistics and probability
-    url: http://edamontology.org/topic_2269
+  - Mathematics
+  - Data architecture, analysis and design
+  - Statistics and probability
   galaxy:
   - description: 'RStudio: '
     title: RStudio 0.3
@@ -19365,13 +17886,10 @@
   description: 'RTG Core: Software for alignment and analysis of next-gen sequencing
     data.'
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  - term: Sequence alignment analysis
-    url: http://edamontology.org/operation_0258
+  - Sequence alignment
+  - Sequence alignment analysis
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genomics
   galaxy: ''
   homepage: https://github.com/RealTimeGenomics/rtg-core
   id: rtg-tools
@@ -19417,17 +17935,12 @@
     for the estimation of isoform abundances directly from a set of reference sequences
     and RNA-seq reads.
   edam-operations:
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
+  - RNA-Seq analysis
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: RNA
-    url: http://edamontology.org/topic_0099
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - RNA-Seq
+  - RNA
+  - Sequencing
+  - Transcriptomics
   galaxy:
   - description: 'Sailfish: transcript quantification from RNA-seq data'
     title: Sailfish 0.10.1.1
@@ -19453,19 +17966,13 @@
   - 1.9.0-gcc-11.3.0                   (D)
   description: A tool for transcript expression quantification from RNA-seq data
   edam-operations:
-  - term: Sequence composition calculation
-    url: http://edamontology.org/operation_0236
-  - term: RNA-Seq quantification
-    url: http://edamontology.org/operation_3800
-  - term: Gene expression analysis
-    url: http://edamontology.org/operation_2495
+  - Sequence composition calculation
+  - RNA-Seq quantification
+  - Gene expression analysis
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - RNA-Seq
+  - Gene expression
+  - Transcriptomics
   galaxy:
   - description: 'Salmon quant: Perform dual-phase, reads or mapping-based estimation
       of transcript abundance from RNA-seq reads'
@@ -19519,19 +18026,13 @@
     version implements some improvements in the original SALSA algorithm. If you want
     to use the old version, it can be found in the old_salsa branch'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
+  - Genome assembly
+  - De-novo assembly
+  - Scaffolding
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: DNA binding sites
-    url: http://edamontology.org/topic_3125
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Sequence assembly
+  - DNA binding sites
+  - Mapping
   galaxy:
   - description: 'SALSA: scaffold long read assemblies with Hi-C'
     title: SALSA 2.3+galaxy3
@@ -19618,17 +18119,12 @@
   description: This tool is a high performance modern robust and fast tool (and library),
     written in the D programming language, for working with SAM, BAM and CRAM formats.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence analysis
+  - Sequence alignment
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - DNA
+  - Sequence analysis
+  - RNA-Seq
   galaxy:
   - description: 'Sample, Slice or Filter BAM: on flags, fields, and tags using Sambamba'
     title: Sample, Slice or Filter BAM 0.7.1+galaxy1
@@ -19654,15 +18150,11 @@
   description: A tool to mark duplicates and extract discordant and split reads from
     SAM files.
   edam-operations:
-  - term: Split read mapping
-    url: http://edamontology.org/operation_3199
+  - Split read mapping
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - DNA
+  - Sequencing
+  - Mapping
   galaxy: ''
   homepage: https://github.com/GregoryFaust/samblaster
   id: samblaster
@@ -19710,29 +18202,18 @@
     and manipulation, sorting, querying, statistics, variant calling, and effect analysis
     amongst other methods.
   edam-operations:
-  - term: Indexing
-    url: http://edamontology.org/operation_0227
-  - term: Editing
-    url: http://edamontology.org/operation_3096
-  - term: Parsing
-    url: http://edamontology.org/operation_1812
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
-  - term: Sorting
-    url: http://edamontology.org/operation_3802
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
-  edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Rare diseases
-    url: http://edamontology.org/topic_3325
+  - Indexing
+  - Editing
+  - Parsing
+  - Visualisation
+  - Formatting
+  - Sorting
+  - Filtering
+  edam-topics:
+  - Mapping
+  - Sequence analysis
+  - Sequencing
+  - Rare diseases
   galaxy:
   - description: 'Samtools split: BAM dataset on readgroups'
     title: Samtools split 1.15.1+galaxy2
@@ -19827,15 +18308,11 @@
     and differential expression testing. The Python-based implementation efficiently
     deals with datasets of more than one million cells.
   edam-operations:
-  - term: Differential gene expression analysis
-    url: http://edamontology.org/operation_3223
+  - Differential gene expression analysis
   edam-topics:
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Cell biology
-    url: http://edamontology.org/topic_2229
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
+  - Gene expression
+  - Cell biology
+  - Genetics
   galaxy:
   - description: 'Remove confounders: with scanpy'
     title: Remove confounders 1.9.6+galaxy3
@@ -19961,19 +18438,13 @@
   description: Pre-processing, quality control, normalization and visualization of
     single-cell RNA-seq data.
   edam-operations:
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
-  - term: Sequence visualisation
-    url: http://edamontology.org/operation_0564
+  - Read pre-processing
+  - Sequencing quality control
+  - Sequence visualisation
   edam-topics:
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
-  - term: Quality affairs
-    url: http://edamontology.org/topic_3393
-  - term: Molecular genetics
-    url: http://edamontology.org/topic_3321
+  - RNA-seq
+  - Quality affairs
+  - Molecular genetics
   galaxy:
   - description: 'Scater: t-SNE plot: of two components'
     title: 'Scater: t-SNE plot 1.22.0'
@@ -20034,21 +18505,14 @@
   description: Scikit-image contains image processing algorithms for SciPy, including
     IO, morphology, filtering, warping, color manipulation, object detection, etc.
   edam-operations:
-  - term: Image analysis
-    url: http://edamontology.org/operation_3443
-  - term: Image annotation
-    url: http://edamontology.org/operation_3553
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  edam-topics:
-  - term: Imaging
-    url: http://edamontology.org/topic_3382
-  - term: Software engineering
-    url: http://edamontology.org/topic_3372
-  - term: Literature and language
-    url: http://edamontology.org/topic_3068
+  - Image analysis
+  - Image annotation
+  - Visualisation
+  - Data handling
+  edam-topics:
+  - Imaging
+  - Software engineering
+  - Literature and language
   galaxy:
   - description: 'Extract image features: with scikit-image'
     title: Extract image features 0.18.1+galaxy0
@@ -20220,11 +18684,9 @@
   description: "SEPP stands for SAT\xE9-Enabled Phylogenetic Placement and addresses\
     \ the problem of phylogenetic placement for meta-genomic short reads"
   edam-operations:
-  - term: Phylogenetic analysis
-    url: http://edamontology.org/operation_0324
+  - Phylogenetic analysis
   edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
+  - Phylogenetics
   galaxy: ''
   homepage: https://github.com/smirarab/sepp
   id: sepp
@@ -20296,19 +18758,13 @@
     usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file
     manipulations.
   edam-operations:
-  - term: DNA transcription
-    url: http://edamontology.org/operation_0372
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: DNA translation
-    url: http://edamontology.org/operation_0371
-  - term: Sequence conversion
-    url: http://edamontology.org/operation_0233
+  - DNA transcription
+  - Sequence trimming
+  - DNA translation
+  - Sequence conversion
   edam-topics:
-  - term: Database management
-    url: http://edamontology.org/topic_3489
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Database management
+  - Sequence analysis
   galaxy:
   - description: 'SeqKit statistics: of FASTA/Q files'
     title: SeqKit statistics 2.8.1+galaxy0
@@ -20359,13 +18815,10 @@
   description: A tool for processing sequences in the FASTA or FASTQ format. It parses
     both FASTA and FASTQ files which can also be optionally compressed by gzip.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Sequence file editing
-    url: http://edamontology.org/operation_2121
+  - Data handling
+  - Sequence file editing
   edam-topics:
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Data management
   galaxy:
   - description: 'seqtk_telo: find telomeres'
     title: seqtk_telo 1.4+galaxy0
@@ -20438,10 +18891,8 @@
     integrate diverse types of single-cell data.
   edam-operations: ''
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - RNA-Seq
+  - Transcriptomics
   galaxy:
   - description: 'Seurat: - toolkit for exploration of single-cell RNA-seq data'
     title: Seurat 4.3.0.1+galaxy1
@@ -20485,13 +18936,10 @@
   bunya: ''
   description: De novo assembly from Oxford Nanopore reads.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
+  - Genome assembly
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Genomics
+  - Sequence assembly
   galaxy:
   - description: 'Shasta: De novo assembly of long read sequencing data'
     title: Shasta 0.6.0+galaxy0
@@ -20521,15 +18969,11 @@
     can take advantage of the pre- and post-processing the Shovill provides with those
     too.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
+  - Genome assembly
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Microbiology
-    url: http://edamontology.org/topic_3301
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Genomics
+  - Microbiology
+  - Sequence assembly
   galaxy:
   - description: 'Shovill: Faster SPAdes assembly of Illumina reads'
     title: Shovill 1.1.0+galaxy2
@@ -20551,13 +18995,10 @@
   description: A clustering approach for identification of enriched domains from histone
     modification ChIP-seq data.
   edam-operations:
-  - term: Sequence contamination filtering
-    url: http://edamontology.org/operation_3187
+  - Sequence contamination filtering
   edam-topics:
-  - term: ChIP-seq
-    url: http://edamontology.org/topic_3169
-  - term: Epigenomics
-    url: http://edamontology.org/topic_3173
+  - ChIP-seq
+  - Epigenomics
   galaxy:
   - description: 'SICER: Statistical approach for the Identification of ChIP-Enriched
       Regions'
@@ -20593,23 +19034,15 @@
     For all PMIDs in each row of a table the according abstracts are saved in additional
     columns.'
   edam-operations:
-  - term: Text mining
-    url: http://edamontology.org/operation_0306
-  - term: Database search
-    url: http://edamontology.org/operation_2421
-  - term: Text annotation
-    url: http://edamontology.org/operation_3778
-  - term: Clustering
-    url: http://edamontology.org/operation_3432
-  edam-topics:
-  - term: Natural language processing
-    url: http://edamontology.org/topic_0218
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
+  - Text mining
+  - Database search
+  - Text annotation
+  - Clustering
+  edam-topics:
+  - Natural language processing
+  - Workflows
+  - Machine learning
+  - Molecular interactions, pathways and networks
   galaxy:
   - description: 'PMIDs to PubTator: binary matrix'
     title: PMIDs to PubTator 0.0.2
@@ -20657,23 +19090,15 @@
     and freely available web application for rapid in silico typing and serovar prediction
     from Salmonella genome assemblies using cgMLST and O and H antigen gene searching.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Multilocus sequence typing
-    url: http://edamontology.org/operation_3840
-  edam-topics:
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Immunoproteins and antigens
-    url: http://edamontology.org/topic_2830
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Zoology
-    url: http://edamontology.org/topic_3500
-  - term: Public health and epidemiology
-    url: http://edamontology.org/topic_3305
+  - Genome assembly
+  - Visualisation
+  - Multilocus sequence typing
+  edam-topics:
+  - Whole genome sequencing
+  - Immunoproteins and antigens
+  - Sequence assembly
+  - Zoology
+  - Public health and epidemiology
   galaxy:
   - description: 'sistr_cmd: Salmonella In Silico Typing Resource commandline tool
       for serovar prediction'
@@ -20787,19 +19212,13 @@
     Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568;
     doi: https://doi.org/10.1101/747568'
   edam-operations:
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: k-mer counting
-    url: http://edamontology.org/operation_3472
+  - Sequence trimming
+  - Genotyping
+  - k-mer counting
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Mathematics
-    url: http://edamontology.org/topic_3315
+  - Sequence assembly
+  - Genetic variation
+  - Mathematics
   galaxy:
   - description: 'Smudgeplot: inference of ploidy and heterozygosity structure using
       whole genome sequencing'
@@ -20828,15 +19247,11 @@
     with a clean and modern domain specific specification language (DSL) in python
     style.
   edam-operations:
-  - term: Service composition
-    url: http://edamontology.org/operation_3762
+  - Service composition
   edam-topics:
-  - term: Bioinformatics
-    url: http://edamontology.org/topic_0091
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Software engineering
-    url: http://edamontology.org/topic_3372
+  - Bioinformatics
+  - Workflows
+  - Software engineering
   galaxy: ''
   homepage: https://snakemake.readthedocs.io/en/stable/index.html
   id: snakemake
@@ -20858,15 +19273,11 @@
   - '2013_11_29'
   description: The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
+  - Gene prediction
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Genetics
-    url: http://edamontology.org/topic_3053
+  - DNA
+  - DNA polymorphism
+  - Genetics
   galaxy:
   - description: 'Train SNAP: ab-initio gene predictor'
     title: Train SNAP 2013_11_29+galaxy1
@@ -20902,19 +19313,13 @@
     \ operative systems | Welcome to snappy\u2019s documentation! \u2014 SNAPPy-HIV1-Subtyping\
     \ 1.0.0 documentation | Free document hosting provided by Read the Docs"
   edam-operations:
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Parsing
-    url: http://edamontology.org/operation_1812
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  edam-topics:
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
-  - term: Public health and epidemiology
-    url: http://edamontology.org/topic_3305
+  - Sequence trimming
+  - Parsing
+  - Genotyping
+  edam-topics:
+  - Phylogenetics
+  - Workflows
+  - Public health and epidemiology
   galaxy: ''
   homepage: https://github.com/PMMAraujo/snappy
   id: snappy
@@ -20936,15 +19341,11 @@
   description: An algorithm for structural variation detection from third generation
     sequencing alignment.
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
-  - term: Structural variation detection
-    url: http://edamontology.org/operation_3228
+  - Sequence analysis
+  - Structural variation detection
   edam-topics:
-  - term: DNA structural variation
-    url: http://edamontology.org/topic_3175
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - DNA structural variation
+  - Sequencing
   galaxy:
   - description: 'sniffles: Structural variation caller using third generation sequencing'
     title: sniffles 1.0.12+galaxy0
@@ -20969,21 +19370,14 @@
   bunya: ''
   description: Rapid haploid variant calling and core SNP phylogeny generation.
   edam-operations:
-  - term: Phylogenetic tree visualisation
-    url: http://edamontology.org/operation_0567
-  - term: Phylogenetic tree generation
-    url: http://edamontology.org/operation_0323
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
+  - Phylogenetic tree visualisation
+  - Phylogenetic tree generation
+  - Variant calling
+  edam-topics:
+  - Genomics
+  - Model organisms
+  - DNA polymorphism
+  - Phylogenetics
   galaxy:
   - description: 'snippy-clean_full_aln: Replace any non-standard sequence characters
       in snippy ''core.full.aln'' file.'
@@ -21056,15 +19450,11 @@
   description: Variant annotation and effect prediction tool. It annotates and predicts
     the effects of variants on genes and proteins (such as amino acid changes).
   edam-operations:
-  - term: SNP detection
-    url: http://edamontology.org/operation_0484
+  - SNP detection
   edam-topics:
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Nucleic acid sites, features and motifs
-    url: http://edamontology.org/topic_3511
+  - DNA polymorphism
+  - Genetic variation
+  - Nucleic acid sites, features and motifs
   galaxy:
   - description: 'SnpEff chromosome-info:: list chromosome names/lengths'
     title: 'SnpEff chromosome-info: 4.3+T.galaxy2'
@@ -21145,13 +19535,10 @@
   bunya: ''
   description: Toolbox that allows you to filter and manipulate annotated vcf files.
   edam-operations:
-  - term: Variant filtering
-    url: http://edamontology.org/operation_3675
+  - Variant filtering
   edam-topics:
-  - term: Data management
-    url: http://edamontology.org/topic_3071
-  - term: Data architecture, analysis and design
-    url: http://edamontology.org/topic_3365
+  - Data management
+  - Data architecture, analysis and design
   galaxy:
   - description: 'SnpSift CaseControl: Count samples are in ''case'' and ''control''
       groups.'
@@ -21197,21 +19584,14 @@
   bunya: ''
   description: SOAPdenovo2 is a next generation sequencing reads de novo assembler.
   edam-operations:
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Sorting
-    url: http://edamontology.org/operation_3802
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Scaffolding
+  - De-novo assembly
+  - Genome assembly
+  - Sorting
+  edam-topics:
+  - Sequence assembly
+  - Sequencing
+  - Metagenomics
   galaxy: ''
   homepage: https://github.com/aquaskyline/SOAPdenovo2
   id: soapdenovo2
@@ -21234,17 +19614,12 @@
   - 4.3.6--h9ee0642_0
   description: Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
   edam-operations:
-  - term: Sequence similarity search
-    url: http://edamontology.org/operation_0346
-  - term: Sequence comparison
-    url: http://edamontology.org/operation_2451
-  - term: Sequence alignment analysis
-    url: http://edamontology.org/operation_0258
+  - Sequence similarity search
+  - Sequence comparison
+  - Sequence alignment analysis
   edam-topics:
-  - term: Metatranscriptomics
-    url: http://edamontology.org/topic_3941
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
+  - Metatranscriptomics
+  - Metagenomics
   galaxy:
   - description: 'Filter with SortMeRNA: of ribosomal RNAs in metatranscriptomic data'
     title: Filter with SortMeRNA 4.3.6+galaxy0
@@ -21293,11 +19668,9 @@
     \ Oxford Nanopore and Sanger reads. Additional contigs can be provided and can\
     \ be used as long reads."
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
+  - Genome assembly
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'SPAdes: genome assembler for genomes of regular and single-cell
       projects'
@@ -21369,11 +19742,9 @@
   description: Spectral Repeat Finder (SRF) is a program to find repeats through an
     analysis of the power spectrum of a given DNA sequence.
   edam-operations:
-  - term: Analysis
-    url: http://edamontology.org/operation_2945
+  - Analysis
   edam-topics:
-  - term: Computational biology
-    url: http://edamontology.org/topic_3307
+  - Computational biology
   galaxy: ''
   homepage: https://webs.iiitd.edu.in/raghava/srf/
   id: srf
@@ -21480,15 +19851,11 @@
   description: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries
     for using data in the INSDC Sequence Read Archives.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - DNA
+  - Genomics
+  - Sequencing
   galaxy:
   - description: 'Download and Extract Reads in BAM: format from NCBI SRA'
     title: Download and Extract Reads in BAM 3.1.1+galaxy0
@@ -21539,19 +19906,13 @@
   description: A fast implementation of the Smith-Waterman algorithm whose API that
     can be flexibly used by programs written in C, C++ and other languages.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
-  edam-topics:
-  - term: Sample collections
-    url: http://edamontology.org/topic_3277
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Data governance
-    url: http://edamontology.org/topic_3571
-  - term: Nucleic acid structure analysis
-    url: http://edamontology.org/topic_0097
+  - Data handling
+  - Sequence alignment
+  edam-topics:
+  - Sample collections
+  - Genomics
+  - Data governance
+  - Nucleic acid structure analysis
   galaxy: ''
   homepage: http://blog.gkno.me/post/42508822069/ssw-library
   id: ssw
@@ -21573,13 +19934,10 @@
     as RADseq, for building genetic maps and conducting population genomics and phylogeography
     analysis.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Population genetics
-    url: http://edamontology.org/topic_3056
+  - Mapping
+  - Population genetics
   galaxy:
   - description: 'Stacks2: clone filter: Identify PCR clones'
     title: 'Stacks2: clone filter 2.55+galaxy4'
@@ -21686,13 +20044,10 @@
   - 2.7.10a--h9ee0642_0
   description: Ultrafast universal RNA-seq data aligner
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence alignment
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - RNA-Seq
+  - Transcriptomics
   galaxy:
   - description: 'RNA STAR: Gapped-read mapper for RNA-seq data'
     title: RNA STAR 2.7.11a+galaxy0
@@ -21744,13 +20099,10 @@
   description: STAR-Fusion, a method that is both fast and accurate in identifying
     fusion transcripts from RNA-Seq data
   edam-operations:
-  - term: Sequence analysis
-    url: http://edamontology.org/operation_2403
+  - Sequence analysis
   edam-topics:
-  - term: Gene structure
-    url: http://edamontology.org/topic_0114
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - Gene structure
+  - RNA-Seq
   galaxy:
   - description: 'STAR-Fusion: detect fusion genes in RNA-Seq data'
     title: STAR-Fusion 0.5.4-3+galaxy1
@@ -21775,15 +20127,11 @@
     novo assembly step to assemble and quantitate full-length transcripts representing
     multiple splice variants for each gene locus.
   edam-operations:
-  - term: Transcriptome assembly
-    url: http://edamontology.org/operation_3258
-  - term: RNA-Seq analysis
-    url: http://edamontology.org/operation_3680
+  - Transcriptome assembly
+  - RNA-Seq analysis
   edam-topics:
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: RNA-seq
-    url: http://edamontology.org/topic_3170
+  - Transcriptomics
+  - RNA-seq
   galaxy:
   - description: 'StringTie: transcript assembly and quantification'
     title: StringTie 2.2.3+galaxy0
@@ -21815,17 +20163,12 @@
     powerful in mapping RNA-seq reads. It supports indel detection and can map reads
     with both fixed and variable lengths.
   edam-operations:
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
-  edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
+  - Read mapping
+  edam-topics:
+  - Sequencing
+  - Mapping
+  - Whole genome sequencing
+  - RNA-Seq
   galaxy: ''
   homepage: http://subread.sourceforge.net/
   id: subread
@@ -21871,15 +20214,11 @@
   description: An agile homology-based approach using a reduced SEED database to report
     the subsystems present in metagenomic samples and profile their abundances.
   edam-operations:
-  - term: Sequence feature detection
-    url: http://edamontology.org/operation_0253
+  - Sequence feature detection
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - DNA
+  - Metagenomics
+  - Sequence analysis
   galaxy: ''
   homepage: http://edwards.sdsu.edu/superfocus/
   id: superfocus
@@ -21904,13 +20243,10 @@
     and calculates the PSI ("Percentage Spliced In") value for each event exploiting
     fast quantification of transcript abundances from multiple samples.
   edam-operations:
-  - term: Splicing model analysis
-    url: http://edamontology.org/operation_2499
+  - Splicing model analysis
   edam-topics:
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: RNA splicing
-    url: http://edamontology.org/topic_3320
+  - Transcriptomics
+  - RNA splicing
   galaxy: ''
   homepage: https://bitbucket.org/regulatorygenomicsupf/suppa/
   id: suppa
@@ -21941,21 +20277,14 @@
     and the reference: deletions, insertions, tandem and interspersed duplications
     and inversions.'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Genotype and phenotype
-    url: http://edamontology.org/topic_0625
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
+  - Genome assembly
+  - Variant calling
+  - Genotyping
+  edam-topics:
+  - Sequence assembly
+  - Genotype and phenotype
+  - Sequencing
+  - DNA polymorphism
   galaxy: ''
   homepage: http://github.com/eldariont/svim-asm
   id: svim-asm
@@ -21989,27 +20318,17 @@
     regions. This distinction is important as rearranged regions are inherited differently
     compared to syntenic regions.'
   edam-operations:
-  - term: Haplotype mapping
-    url: http://edamontology.org/operation_0487
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
-  - term: Sequence assembly
-    url: http://edamontology.org/operation_0310
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
-  edam-topics:
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: DNA structural variation
-    url: http://edamontology.org/topic_3175
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Haplotype mapping
+  - Variant calling
+  - Genotyping
+  - Sequence assembly
+  - Read mapping
+  edam-topics:
+  - DNA polymorphism
+  - Sequence assembly
+  - DNA structural variation
+  - Mapping
+  - Sequencing
   galaxy: ''
   homepage: https://schneebergerlab.github.io/syri/
   id: syri
@@ -22095,23 +20414,15 @@
   description: Targetfinder.org provides a web based resource that allows users to
     find genes that have a similar expression to a query gene signature.
   edam-operations:
-  - term: Gene prediction
-    url: http://edamontology.org/operation_2454
-  - term: Gene expression profiling
-    url: http://edamontology.org/operation_0314
-  - term: Gene expression analysis
-    url: http://edamontology.org/operation_2495
-  edam-topics:
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: Small molecules
-    url: http://edamontology.org/topic_0154
-  - term: Gene regulation
-    url: http://edamontology.org/topic_0204
+  - Gene prediction
+  - Gene expression profiling
+  - Gene expression analysis
+  edam-topics:
+  - Gene expression
+  - Transcription factors and regulatory sites
+  - Gene transcripts
+  - Small molecules
+  - Gene regulation
   galaxy:
   - description: 'TargetFinder: plant small RNA target prediction tool'
     title: TargetFinder 1.7.0+galaxy1
@@ -22233,15 +20544,11 @@
     that lets researchers push the state-of-the-art in ML and developers easily build
     and deploy ML powered applications'
   edam-operations:
-  - term: Standardisation and normalisation
-    url: http://edamontology.org/operation_3435
+  - Standardisation and normalisation
   edam-topics:
-  - term: Machine learning
-    url: http://edamontology.org/topic_3474
-  - term: Pathology
-    url: http://edamontology.org/topic_0634
-  - term: Biomarkers
-    url: http://edamontology.org/topic_3360
+  - Machine learning
+  - Pathology
+  - Biomarkers
   galaxy: ''
   homepage: https://www.tensorflow.org
   id: tensorflow
@@ -22274,19 +20581,13 @@
     on database/ and bin/. You can add the directory to PATH or soft link TEsorter.py
     to PATH'
   edam-operations:
-  - term: Phylogenetic tree reconstruction
-    url: http://edamontology.org/operation_3478
-  edam-topics:
-  - term: Protein folds and structural domains
-    url: http://edamontology.org/topic_0736
-  - term: Phylogenetics
-    url: http://edamontology.org/topic_3293
-  - term: Transcription factors and regulatory sites
-    url: http://edamontology.org/topic_0749
-  - term: Plant biology
-    url: http://edamontology.org/topic_0780
-  - term: Model organisms
-    url: http://edamontology.org/topic_0621
+  - Phylogenetic tree reconstruction
+  edam-topics:
+  - Protein folds and structural domains
+  - Phylogenetics
+  - Transcription factors and regulatory sites
+  - Plant biology
+  - Model organisms
   galaxy: ''
   homepage: https://github.com/zhangrengang/TEsorter
   id: tesorter
@@ -22404,19 +20705,13 @@
   description: Open-source, crossplatform tool that converts Thermo RAW files into
     open file formats such as MGF and to the HUPO-PSI standard file format mzML
   edam-operations:
-  - term: Conversion
-    url: http://edamontology.org/operation_3434
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
-  - term: Peak detection
-    url: http://edamontology.org/operation_3215
+  - Conversion
+  - Filtering
+  - Peak detection
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Proteomics
+  - Proteomics experiment
+  - Metabolomics
   galaxy:
   - description: 'Thermo: RAW file converter'
     title: Thermo 1.3.4+galaxy0
@@ -22441,17 +20736,12 @@
     exon-exon splice junctions. It is built on the ultrafast short read mapping program
     Bowtie. A stable SAMtools version is now packaged with the program.
   edam-operations:
-  - term: Splice site prediction
-    url: http://edamontology.org/operation_0433
-  - term: Read mapping
-    url: http://edamontology.org/operation_3198
+  - Splice site prediction
+  - Read mapping
   edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
-  - term: Rare diseases
-    url: http://edamontology.org/topic_3325
+  - RNA-Seq
+  - Mapping
+  - Rare diseases
   galaxy:
   - description: 'TopHat: Gapped-read mapper for RNA-seq data'
     title: TopHat 2.1.1
@@ -22481,8 +20771,7 @@
   description: TotalView is a debugger for High Performance Computing applications.
   edam-operations: ''
   edam-topics:
-  - term: Computer science
-    url: http://edamontology.org/topic_3316
+  - Computer science
   galaxy: ''
   homepage: https://totalview.io/
   id: totalview
@@ -22506,25 +20795,16 @@
     Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat
     and Cufflinks.
   edam-operations:
-  - term: Coding region prediction
-    url: http://edamontology.org/operation_0436
-  - term: de Novo sequencing
-    url: http://edamontology.org/operation_3644
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
+  - Coding region prediction
+  - de Novo sequencing
+  - De-novo assembly
+  edam-topics:
+  - Genomics
+  - Gene transcripts
+  - RNA-Seq
+  - Gene expression
+  - Sequence assembly
+  - Whole genome sequencing
   galaxy:
   - description: 'TransDecoder: finds coding regions within transcripts'
     title: TransDecoder 5.5.0+galaxy2
@@ -22547,15 +20827,11 @@
     graphical interface and access to three different analysis methods that allow
     the user to determine essentiality in a single condition as well as between conditions.
   edam-operations:
-  - term: Transposon prediction
-    url: http://edamontology.org/operation_0427
+  - Transposon prediction
   edam-topics:
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Mobile genetic elements
-    url: http://edamontology.org/topic_0798
+  - DNA
+  - Sequencing
+  - Mobile genetic elements
   galaxy:
   - description: 'TRANSIT Tn5Gaps: - determine essential genes'
     title: TRANSIT Tn5Gaps 3.0.2+galaxy1
@@ -22591,10 +20867,8 @@
   description: Institute for Systems Biology "Trans-Proteomic Pipeline"
   edam-operations: ''
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
+  - Proteomics
+  - Proteomics experiment
   galaxy:
   - description: 'Protein Prophet: Calculate Protein Prophet statistics on search
       results'
@@ -22685,13 +20959,10 @@
     determines a consensus pattern for the smallest repetitive unit in the tandem
     repeat.
   edam-operations:
-  - term: Repeat sequence detection
-    url: http://edamontology.org/operation_0379
+  - Repeat sequence detection
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequence composition, complexity and repeats
-    url: http://edamontology.org/topic_0157
+  - Sequence analysis
+  - Sequence composition, complexity and repeats
   galaxy: ''
   homepage: http://tandem.bu.edu/trf/trf.html
   id: trf
@@ -22713,15 +20984,11 @@
   description: Tool for the automated removal of spurious sequences or poorly aligned
     regions from a multiple sequence alignment.
   edam-operations:
-  - term: Multiple sequence alignment
-    url: http://edamontology.org/operation_0492
+  - Multiple sequence alignment
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
+  - Sequence analysis
+  - Sequencing
+  - Sequence sites, features and motifs
   galaxy: ''
   homepage: http://trimal.cgenomics.org
   id: trimal
@@ -22745,15 +21012,11 @@
     and adapter trimming to FastQ files, with some extra functionality for MspI-digested
     RRBS-type (Reduced Representation Bisufite-Seq) libraries.
   edam-operations:
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Primer removal
-    url: http://edamontology.org/operation_3237
-  - term: Read pre-processing
-    url: http://edamontology.org/operation_3219
+  - Sequence trimming
+  - Primer removal
+  - Read pre-processing
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'Trim Galore!: Quality and adapter trimmer of reads'
     title: Trim Galore! 0.6.7+galaxy0
@@ -22775,15 +21038,11 @@
   - 0.39-java-11
   description: A flexible read trimming tool for Illumina NGS data
   edam-operations:
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
+  - Sequence trimming
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
-  - term: Data quality management
-    url: http://edamontology.org/topic_3572
+  - Sequencing
+  - Sequence analysis
+  - Data quality management
   galaxy:
   - description: 'Trimmomatic: flexible read trimming tool for Illumina NGS data'
     title: Trimmomatic 0.36.6
@@ -22813,15 +21072,11 @@
     tools, inchworm an assembler, chrysalis which pools contigs and butterfly which
     amongst others compacts a graph resulting from butterfly with reads.
   edam-operations:
-  - term: Transcriptome assembly
-    url: http://edamontology.org/operation_3258
+  - Transcriptome assembly
   edam-topics:
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Gene transcripts
-    url: http://edamontology.org/topic_3512
+  - Transcriptomics
+  - Gene expression
+  - Gene transcripts
   galaxy:
   - description: 'Generate SuperTranscripts: from a Trinity assembly'
     title: Generate SuperTranscripts 2.15.1+galaxy0
@@ -22892,13 +21147,10 @@
     of transcriptomes, particularly de novo assembled transcriptomes, from model or
     non-model organisms.
   edam-operations:
-  - term: Gene functional annotation
-    url: http://edamontology.org/operation_3672
+  - Gene functional annotation
   edam-topics:
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Transcriptomics
-    url: http://edamontology.org/topic_3308
+  - Gene expression
+  - Transcriptomics
   galaxy:
   - description: 'Trinotate: functional transcript annotation'
     title: Trinotate 3.2.2+galaxy0
@@ -22922,17 +21174,12 @@
   bunya: ''
   description: A program for improved detection of transfer RNA genes in genomic sequence.
   edam-operations:
-  - term: tRNA gene prediction
-    url: http://edamontology.org/operation_0464
-  - term: Sequence feature detection
-    url: http://edamontology.org/operation_0253
+  - tRNA gene prediction
+  - Sequence feature detection
   edam-topics:
-  - term: RNA
-    url: http://edamontology.org/topic_0099
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - RNA
+  - Genomics
+  - Sequence analysis
   galaxy:
   - description: 'tRNA prediction: (tRNAscan)'
     title: tRNA prediction 0.4
@@ -22958,25 +21205,16 @@
   bunya: ''
   description: 'Trycycler: consensus long-read assemblies for bacterial genomes'
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Sequence trimming
-    url: http://edamontology.org/operation_3192
-  - term: Scaffold gap completion
-    url: http://edamontology.org/operation_3217
-  - term: Sequence assembly validation
-    url: http://edamontology.org/operation_3180
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: DNA
-    url: http://edamontology.org/topic_0654
-  - term: Human biology
-    url: http://edamontology.org/topic_2815
-  - term: Whole genome sequencing
-    url: http://edamontology.org/topic_3673
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genome assembly
+  - Sequence trimming
+  - Scaffold gap completion
+  - Sequence assembly validation
+  edam-topics:
+  - Sequence assembly
+  - DNA
+  - Human biology
+  - Whole genome sequencing
+  - Genomics
   galaxy:
   - description: 'Trycycler subsample: make a maximally-independent read subsets of
       an appropiate depth for your genome'
@@ -23017,8 +21255,7 @@
     Browser project.
   edam-operations: ''
   edam-topics:
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Sequence analysis
   galaxy:
   - description: 'faSplit: Split a FASTA file'
     title: faSplit 377
@@ -23097,15 +21334,11 @@
   bunya: ''
   description: Tools for handling Unique Molecular Identifiers in NGS data sets.
   edam-operations:
-  - term: Sequencing quality control
-    url: http://edamontology.org/operation_3218
+  - Sequencing quality control
   edam-topics:
-  - term: NGS
-    url: http://edamontology.org/topic_3168
-  - term: Sequence sites, features and motifs
-    url: http://edamontology.org/topic_0160
-  - term: Quality affairs
-    url: http://edamontology.org/topic_3393
+  - NGS
+  - Sequence sites, features and motifs
+  - Quality affairs
   galaxy:
   - description: 'UMI-tools whitelist: Extract cell barcodes from FASTQ files'
     title: UMI-tools whitelist 1.1.2+galaxy2
@@ -23142,19 +21375,13 @@
   description: A tool for assembling bacterial genomes from a combination of short
     (2nd generation) and long (3rd generation) sequencing reads.
   edam-operations:
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: Aggregation
-    url: http://edamontology.org/operation_3436
+  - Genome assembly
+  - Aggregation
   edam-topics:
-  - term: Microbiology
-    url: http://edamontology.org/topic_3301
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Microbiology
+  - Genomics
+  - Sequencing
+  - Sequence assembly
   galaxy:
   - description: 'Create assemblies with Unicycler: pipeline for bacterial genomes'
     title: Create assemblies with Unicycler 0.5.0+galaxy1
@@ -23178,19 +21405,13 @@
   bunya: ''
   description: Metaproteomics data analysis with a focus on interactive data visualizations.
   edam-operations:
-  - term: Prediction and recognition
-    url: http://edamontology.org/operation_2423
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
+  - Prediction and recognition
+  - Visualisation
   edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteogenomics
-    url: http://edamontology.org/topic_3922
-  - term: Biodiversity
-    url: http://edamontology.org/topic_3050
-  - term: Workflows
-    url: http://edamontology.org/topic_0769
+  - Proteomics
+  - Proteogenomics
+  - Biodiversity
+  - Workflows
   galaxy:
   - description: 'Unipept: retrieve taxonomy for peptides'
     title: Unipept 4.5.1
@@ -23286,15 +21507,11 @@
     protists, metazoa and bacteria.  There is a web and a REST API version but the
     most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology
   edam-operations:
-  - term: SNP annotation
-    url: http://edamontology.org/operation_3661
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
+  - SNP annotation
+  - Genetic variation analysis
   edam-topics:
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
+  - Genetic variation
+  - Genomics
   galaxy: ''
   homepage: http://www.ensembl.org/vep
   id: vep
@@ -23315,13 +21532,10 @@
   description: VarScan, an open source tool for variant detection that is compatible
     with several short read align-ers.
   edam-operations:
-  - term: Variant calling
-    url: http://edamontology.org/operation_3227
+  - Variant calling
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
+  - Sequencing
+  - DNA polymorphism
   galaxy:
   - description: 'VarScan copynumber: Determine relative tumor copy number from tumor-normal
       pileups'
@@ -23402,13 +21616,10 @@
   - 1.0.3-foss-2021a-r-4.1.0
   description: API and command line utilities for the manipulation of VCF files.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
+  - Data handling
   edam-topics:
-  - term: Genomics
-    url: http://edamontology.org/topic_0622
-  - term: Data management
-    url: http://edamontology.org/topic_3071
+  - Genomics
+  - Data management
   galaxy:
   - description: 'VCFtoTab-delimited:: Convert VCF data into TAB-delimited format'
     title: 'VCFtoTab-delimited: 1.0.0_rc3+galaxy0'
@@ -23511,15 +21722,11 @@
   description: Provide easily accessible methods for working with complex genetic
     variation data in the form of VCF files.
   edam-operations:
-  - term: Data handling
-    url: http://edamontology.org/operation_2409
-  - term: Variant filtering
-    url: http://edamontology.org/operation_3675
-  - term: Genetic variation analysis
-    url: http://edamontology.org/operation_3197
+  - Data handling
+  - Variant filtering
+  - Genetic variation analysis
   edam-topics:
-  - term: Genetic variation
-    url: http://edamontology.org/topic_0199
+  - Genetic variation
   galaxy:
   - description: 'Intersect: multiple VCF datasets'
     title: Intersect 0.1.1
@@ -23548,11 +21755,9 @@
   description: A de novo genomic assembler specially designed for short read sequencing
     technologies, such as Solexa or 454 or SOLiD.
   edam-operations:
-  - term: Formatting
-    url: http://edamontology.org/operation_0335
+  - Formatting
   edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - Sequence assembly
   galaxy:
   - description: 'velvetg: Velvet sequence assembler for very short reads'
     title: velvetg 1.2.10.2
@@ -23646,15 +21851,11 @@
     exact and global alignment searching, shuffling, subsampling and sorting. It also
     supports FASTQ file analysis, filtering and conversion.
   edam-operations:
-  - term: DNA mapping
-    url: http://edamontology.org/operation_2520
-  - term: Chimera detection
-    url: http://edamontology.org/operation_0450
+  - DNA mapping
+  - Chimera detection
   edam-topics:
-  - term: Metagenomics
-    url: http://edamontology.org/topic_3174
-  - term: Sequence analysis
-    url: http://edamontology.org/topic_0080
+  - Metagenomics
+  - Sequence analysis
   galaxy:
   - description: 'VSearch clustering: '
     title: VSearch clustering 2.8.3.0
@@ -23721,13 +21922,10 @@
     called haplotype assembly. It is especially suitable for long reads, but works
     also well with short reads.
   edam-operations:
-  - term: Genotyping
-    url: http://edamontology.org/operation_3196
+  - Genotyping
   edam-topics:
-  - term: DNA polymorphism
-    url: http://edamontology.org/topic_2885
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
+  - DNA polymorphism
+  - Sequence assembly
   galaxy: ''
   homepage: http://whatshap.readthedocs.io
   id: whatshap
@@ -23752,13 +21950,10 @@
   description: windowmasker identifies and masks highly repetitive DNA sequences in
     a genome, using only the sequence of the genome itself.
   edam-operations:
-  - term: Repeat sequence detection
-    url: http://edamontology.org/operation_0379
-  - term: Repeat sequence analysis
-    url: http://edamontology.org/operation_0237
+  - Repeat sequence detection
+  - Repeat sequence analysis
   edam-topics:
-  - term: Sequencing
-    url: http://edamontology.org/topic_3168
+  - Sequencing
   galaxy:
   - description: 'WindowMasker ustat: Mask sequences using a WindowMasker unit counts
       table'
@@ -23786,11 +21981,9 @@
     on top of minimap2 codebase, and since then we have incorporated the following
     two ideas to improve mapping accuracy within repeats
   edam-operations:
-  - term: Sequence alignment
-    url: http://edamontology.org/operation_0292
+  - Sequence alignment
   edam-topics:
-  - term: Mapping
-    url: http://edamontology.org/topic_0102
+  - Mapping
   galaxy: ''
   homepage: https://github.com/marbl/Winnowmap
   id: winnowmap
@@ -23815,27 +22008,17 @@
     metabolomics. It includes preprocessing, normalization, quality control, statistical
     analysis of LC/MS, FIA-MS, GC/MS and NMR data.
   edam-operations:
-  - term: Visualisation
-    url: http://edamontology.org/operation_0337
-  - term: Statistical calculation
-    url: http://edamontology.org/operation_2238
-  - term: Chromatogram visualisation
-    url: http://edamontology.org/operation_3203
-  - term: Spectral analysis
-    url: http://edamontology.org/operation_3214
-  - term: Annotation
-    url: http://edamontology.org/operation_0226
-  - term: Mass spectrum visualisation
-    url: http://edamontology.org/operation_3694
-  - term: Enrichment analysis
-    url: http://edamontology.org/operation_3501
-  edam-topics:
-  - term: Systems biology
-    url: http://edamontology.org/topic_2259
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
-  - term: Computational biology
-    url: http://edamontology.org/topic_3307
+  - Visualisation
+  - Statistical calculation
+  - Chromatogram visualisation
+  - Spectral analysis
+  - Annotation
+  - Mass spectrum visualisation
+  - Enrichment analysis
+  edam-topics:
+  - Systems biology
+  - Metabolomics
+  - Computational biology
   galaxy:
   - description: 'Determine_batch_correction: to choose between linear, lowess and
       loess methods'
@@ -23974,27 +22157,17 @@
     NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput,
     untargeted analyte profiling.
   edam-operations:
-  - term: Mass spectrum visualisation
-    url: http://edamontology.org/operation_3694
-  - term: Label-free quantification
-    url: http://edamontology.org/operation_3634
-  - term: Validation
-    url: http://edamontology.org/operation_2428
-  - term: Filtering
-    url: http://edamontology.org/operation_3695
-  - term: Chromatographic alignment
-    url: http://edamontology.org/operation_3628
-  - term: Peak detection
-    url: http://edamontology.org/operation_3215
-  - term: Chromatogram visualisation
-    url: http://edamontology.org/operation_3203
-  edam-topics:
-  - term: Biological imaging
-    url: http://edamontology.org/topic_3383
-  - term: Data visualisation
-    url: http://edamontology.org/topic_0092
-  - term: Metabolomics
-    url: http://edamontology.org/topic_3172
+  - Mass spectrum visualisation
+  - Label-free quantification
+  - Validation
+  - Filtering
+  - Chromatographic alignment
+  - Peak detection
+  - Chromatogram visualisation
+  edam-topics:
+  - Biological imaging
+  - Data visualisation
+  - Metabolomics
   galaxy:
   - description: 'xcms get a sampleMetadata file: which need to be filled with extra
       information'
@@ -24067,23 +22240,15 @@
     Python package for detection of differential RNA modifications from direct RNA
     sequencing.'
   edam-operations:
-  - term: Quantification
-    url: http://edamontology.org/operation_3799
-  - term: Expression analysis
-    url: http://edamontology.org/operation_2495
-  - term: DMR identification
-    url: http://edamontology.org/operation_3809
-  edam-topics:
-  - term: RNA-Seq
-    url: http://edamontology.org/topic_3170
-  - term: RNA
-    url: http://edamontology.org/topic_0099
-  - term: Gene expression
-    url: http://edamontology.org/topic_0203
-  - term: Genotype and phenotype
-    url: http://edamontology.org/topic_0625
-  - term: Molecular interactions, pathways and networks
-    url: http://edamontology.org/topic_0602
+  - Quantification
+  - Expression analysis
+  - DMR identification
+  edam-topics:
+  - RNA-Seq
+  - RNA
+  - Gene expression
+  - Genotype and phenotype
+  - Molecular interactions, pathways and networks
   galaxy: ''
   homepage: https://github.com/GoekeLab/xpore
   id: xpore
@@ -24103,21 +22268,14 @@
   bunya: ''
   description: Matches tandem mass spectra with peptide sequences.
   edam-operations:
-  - term: Blind peptide database search
-    url: http://edamontology.org/operation_3647
-  - term: PTM identification
-    url: http://edamontology.org/operation_3645
-  - term: Peptide identification
-    url: http://edamontology.org/operation_3631
-  - term: Peptide database search
-    url: http://edamontology.org/operation_3646
-  - term: Protein identification
-    url: http://edamontology.org/operation_3767
-  edam-topics:
-  - term: Proteomics
-    url: http://edamontology.org/topic_0121
-  - term: Proteomics experiment
-    url: http://edamontology.org/topic_3520
+  - Blind peptide database search
+  - PTM identification
+  - Peptide identification
+  - Peptide database search
+  - Protein identification
+  edam-topics:
+  - Proteomics
+  - Proteomics experiment
   galaxy:
   - description: 'X!Tandem MSMS Search: Run an X!Tandem Search'
     title: X!Tandem MSMS Search 1.1.1
@@ -24166,17 +22324,12 @@
     for contig joining detection which considers the topological distribution of Hi-C
     signals aiming to distinguish real interaction signals from mapping noises.
   edam-operations:
-  - term: Scaffolding
-    url: http://edamontology.org/operation_3216
-  - term: Genome assembly
-    url: http://edamontology.org/operation_0525
-  - term: De-novo assembly
-    url: http://edamontology.org/operation_0524
-  edam-topics:
-  - term: Sequence assembly
-    url: http://edamontology.org/topic_0196
-  - term: DNA binding sites
-    url: http://edamontology.org/topic_3125
+  - Scaffolding
+  - Genome assembly
+  - De-novo assembly
+  edam-topics:
+  - Sequence assembly
+  - DNA binding sites
   galaxy:
   - description: 'YAHS: yet another HI-C scaffolding tool'
     title: YAHS 1.2a.2+galaxy1