DISEASES (https://diseases.jensenlab.org/) is a weekly updated web re…

…source that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. We further unify the evidence by assigning confidence scores that facilitate comparison of the different types and sources of evidence. It is under the CC-BY license.

This import brings in all of the DISEASES data sources: experimental, manual, and text mining curation. It divides each source into coding and non-coding genes and formats it into csv+tmcf pairs. These formatted data have passed the json tool (output report.jsons listed below) and the internal v3 staging tool.

PiperOrigin-RevId: 587926885

biomedical_schema/genome_annotation.mcf

@@ -96,6 +96,13 @@ typeOf: schema:Class
 subClassOf: dcs:GenomeAnnotation
 description: "A recorded nucleotide on the positive strand of a denoted genome assembly."
 
+Node: dcid:NonCodingRNA
+name: "NonCodingRNA"
+typeOf: schema:Class
+subClassOf: dcs:Gene
+description: "A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR."
+descriptionUrl: "https://en.wikipedia.org/wiki/Non-coding_RNA"
+
 Node: dcid:RNATranscript
 name: "RNATranscript"
 typeOf: schema:Class
@@ -1117,3 +1124,46 @@ name: "regressionSlope"
 typeOf: schema:Property
 rangeIncludes: schema:Number
 domainIncludes: dcs:StatisticalVariable
+
+Node: dcid:nonCodingRNAType
+name: "nonCodingRNAType"
+typeOf: schema:Property
+domainIncludes: dcs:NonCodingRNA
+rangeIncludes: dcs:NonCodingRNATypeEnum
+description: "A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR."
+descriptionUrl: "https://en.wikipedia.org/wiki/Non-coding_RNA"
+
+Node: dcid:associationSource
+name: "associationSource"
+typeOf: schema:Property
+domainIncludes: schema:Thing
+rangeIncludes: schema:Text
+description: "The organization that reported an association between two things."
+
+Node: dcid:associationType
+name: "associationType"
+typeOf: schema:Property
+domainIncludes: schema:Thing
+rangeIncludes: dcs:AssociationTypeEnum
+description: "The way by which an association between two entities is made."
+
+Node: dcid:confidence
+name: "confidence"
+typeOf: schema:Property
+domainIncludes: schema:Thing
+rangeIncludes: schema:Text
+description: "The level of confidence that a given result is accurate."
+
+Node: dcid:synonym
+name: "synonym"
+typeOf: schema:Property
+domainIncludes: schema:Thing
+rangeIncludes: schema:Text
+description: "Alternative names for the given entity."
+
+Node: dcid:zScore
+name: "zScore"
+typeOf: schema:Property
+domainIncludes: schema:Thing
+rangeIncludes: schema:Text
+description: "A statistical measurement that describes a value's relationship to the mean of a group of values in a normal distribution curve."

biomedical_schema/genome_annotation_enum.mcf

@@ -1157,3 +1157,80 @@ Node: dcid:DNASequenceRoleNovelPatch
 name: "DNASequenceRoleNovel-patch"
 typeOf: dcs:DNASequenceRoleEnum
 description: "The object is a novel patch to the assembly-unit scaffold."
+
+Node: dcid:AssociationTypeEnum
+name: "AssociationTypeEnum"
+typeOf: schema:Class
+subClassOf: dcs:Enumeration
+description: "The way by which an association between two entities is made."
+
+Node: dcid:AssociationTypeExperiment
+typeOf: dcs:AssociationTypeEnum
+name: "Experiment"
+description: "An association between two things was made as a result of a scientific experiment or screening."
+
+Node: dcid:AssociationTypeManuallyCurated
+typeOf: dcs:AssociationTypeEnum
+name: "Manually Curated"
+description: "An association between two things was made through manual curation of scientific literature or database annotations."
+
+Node: dcid:AssociationTypeTextMining
+typeOf: dcs:AssociationTypeEnum
+name: "Text Mining"
+description: "An association between two things was made through automated text mining of the scientific literature."
+
+Node: dcid:NonCodingRNATypeEnum
+name: "NonCodingRNATypeEnum"
+typeOf: schema:Class
+subClassOf: dcs:Enumeration
+description: "A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR."
+descriptionUrl: "https://en.wikipedia.org/wiki/Non-coding_RNA"
+
+Node: dcid:NonCodingRNATypeRibosomalRNA
+typeOf: dcs:NonCodingRNATypeEnum
+name: "Ribosomal RNA"
+shortDisplayName: "rRNA"
+description: "Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells."
+descriptionUrl: "https://en.wikipedia.org/wiki/Ribosomal_RNA"
+
+Node: dcid:NonCodingRNATypeLongNonCodingRNA
+typeOf: dcs:NonCodingRNATypeEnum
+name: "Long NonCoding RNA"
+shortDisplayName: "lncRNA"
+description: "Long noncoding RNA (LncRNA) is a large class of RNA molecules with size larger than 200 nucleotides. They exhibit cellular functions although having no protein-coding capability."
+descriptionUrl: "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-noncoding-rna"
+
+Node: dcid:NonCodingRNATypeLongIntergenicNonCodingRNA
+typeOf: dcs:NonCodingRNATypeEnum
+name: "Long Intergenic NonCoding RNA"
+shortDisplayName: "lincRNA"
+description: "Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences of lncRNA which do not overlap protein-coding genes."
+descriptionUrl: "https://en.wikipedia.org/wiki/Long_non-coding_RNA"
+
+Node: dcid:NonCodingRNATypeSmallNucleolarRNA
+typeOf: dcs:NonCodingRNATypeEnum
+name: "Small Nucleolar RNA"
+shortDisplayName: "snoRNA"
+description: "Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs."
+descriptionUrl: "https://en.wikipedia.org/wiki/Small_nucleolar_RNA"
+
+Node: dcid:NonCodingRNATypeMicroRNA
+typeOf: dcs:NonCodingRNATypeEnum
+name: "MicroRNA"
+shortDisplayName: "miRNA"
+description: "MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides."
+descriptionUrl: "https://en.wikipedia.org/wiki/MicroRNA"
+
+Node: dcid:NonCodingRNATypeCircularRNA
+typeOf: dcs:NonCodingRNATypeEnum
+name: "CircularRNA"
+shortDisplayName: "circRNA"
+description: "Circular RNA (or circRNA) is a type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop."
+descriptionUrl: "https://en.wikipedia.org/wiki/Circular_RNA"
+
+Node: dcid:NonCodingRNATypePromoterAssociatedRNA
+typeOf: dcs:NonCodingRNATypeEnum
+name: "Promoter-Associated RNA"
+shortDisplayName: "pRNA"
+description: "Promoter-associated RNAs (pRNAs) are a family of ~90–100 nt-long divergent RNAs overlapping the promoter of the rRNA (rDNA) operon."
+descriptionUrl: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929421/"