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Removes ABCD Antibody because I am unable to determine the licensing …
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…under which the data was made available. It is not stated in the original publication, on the website, nor on the host sever Expasy. The group in charge Geneva Antibody Facility did not respond to the inquiry regarding the license under which the data is made available. I decided to remove it from the graph out of abundance of caution. I removed the schema regarding this import as well

PiperOrigin-RevId: 579986695
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@spiekos @copybara-github
spiekos authored and copybara-github committed Nov 7, 2023
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147 changes: 0 additions & 147 deletions biomedical_schema/chemical_compound.mcf
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Expand Up @@ -778,153 +778,6 @@ descriptionUrl: "https://www.proteinatlas.org/about/assays+annotation#if_reliabi
rangeIncludes: dcs:HumanProteinOccurrenceReliabilityEnum
domainIncludes: dcs:HumanProteinOccurrence

Node: dcid:Antibody
name: "Antibody"
typeOf: schema:Class
subClassOf: dcs:Protein
description: "An antibody is a kind of protective protein which is produced by the immune system when substances from the outer source invade the living organisms. The process of producing the antibodies is called immune response."

Node: dcid:Antigen
name: "Antigen"
typeOf: schema:Class
subClassOf: dcs:ChemicalCompound
description: "The invading substances from the outer source which causes the immune response. It refers to a molecule or molecule structure which may interact with the immune cell antigen receptor or antibody. "
descriptionUrl:"https://en.wikipedia.org/wiki/Antigen"

Node: dcid:recognizesAntigen
typeOf: schema:Property
name: "recognizesAntigen"
description: "The targeting antigen of the antibody."
rangeIncludes: dcs:Protein
domainIncludes:dcs:Antibody
# rangeIncludes proteins with links to UniProt, chemicals with IDs to ChEBI and a few samples to other databases (InterPro, NCBI, Prosite, UniProt-Subcell).

Node: dcid:antigenType
typeOf: schema:Property
name: "antigenType"
description: "The type of the antigen for an antibody which includes protein, chemical compound and other types. "
rangeIncludes: dcs:Protein
domainIncludes:dcs:Antibody

Node: dcid:antibodyType
typeOf: schema:Property
name: "antibodyType"
description: "The type of antibody, including bispecific antibody, nanobody and DARPins. "
rangeIncludes: dcs:AntibodyTypeEnum
domainIncludes:dcs:Antibody

Node: dcid:antibodyApplication
typeOf: schema:Property
name: "antibodyApplication"
description: "The applications of the antibody in the experiments, such as ELISA, Immunofluorescence, Immunoprecipitation, etc."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody

Node: dcid:epitope
typeOf: schema:Property
name: "epitope"
description: "Also known as antigenic determinant. It is the recognizing part of an antigen by the interacting immune cell antigen receptor or the antibody."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://en.wikipedia.org/wiki/Epitope"

Node: dcid:abcdID
typeOf: schema:Property
name: "abcdID"
description: "The accession identifier of the antibody in the ABCD antibody database. "
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://web.expasy.org/abcd/"

Node: dcid:patentID
typeOf: schema:Property
name: "patentID"
description: "The identifier of patent in PATENTSCOPE. Using PATENTSCOPE you can search 90 million patent documents including 3.9 million published international patent applications (PCT)."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://patentscope.wipo.int/search/en/search.jsf"

Node: dcid:cellosaurusID
typeOf: schema:Property
name: "cellosaurusID"
description: "The identifier of cell line in Cellosaurus. The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://web.expasy.org/cellosaurus/"

Node: dcid:imgtMonoclonalAntibodiesDBID
typeOf: schema:Property
name: "imgtMonoclonalAntibodiesDBID"
description: "The identifier for therapeutic monoclonal antibodies in IMGT/mAb-DB. IMGT/mAb-DB is the IMGT monoclonal antibodies (mAb) database."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"http://www.imgt.org/mAb-DB/"

Node: dcid:neuroMabID
typeOf: schema:Property
name: "neuroMabID"
description: "The identifier for mouse monoclonal antibodies in NeuroMab. The UC Davis/NIH NeuroMab Facility generates mouse monoclonal antibodies extensively validated for use in the mammalian brain."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"http://neuromab.ucdavis.edu/"

Node: dcid:ginasID
typeOf: schema:Property
name: "ginasID"
description: "The identifier for substances found in medicines in Ginas. The main goal of ginas is the production of software, called G-SRS, to assist agencies in registering and documenting information about substances found in medicines."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://tripod.nih.gov/ginas/#/"

Node: dcid:recombinantAntibodyNetworkID
typeOf: schema:Property
name: "recombinantAntibodyNetworkID"
description: "The identifier for antibodies in Recombinant Antibody Network (RAN). The RAN is an international consortium of three expert centers at the University of Chicago, University of Toronto, and the University of California at San Francisco (UCSF) unified under a common set of goals, technologies, and operational procedures."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://recombinant-antibodies.org/"

Node: dcid:addgeneID
typeOf: schema:Property
name: "addgeneID"
description: "The identifier for antibodies in Addgene. They distribute 89,594 plasmids on behalf of 4,322 labs from around the world. They also produce 480 ready-to-use viral vectors from our plasmid collection."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://www.addgene.org/"

Node: dcid:interProID
typeOf: schema:Property
name: "interProID"
description: "The identifier for protein families in Addgene. InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://www.ebi.ac.uk/interpro/"

Node: dcid:ncbiTXID
typeOf: schema:Property
name: "ncbiTXID"
description: "The txid identifier in NCBI Taxonomy Browser. The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi"
# example NCBI:txid46170

Node: dcid:uniProtSubcellularID
typeOf: schema:Property
name: "uniProtSubcellularID"
description: "The identifier of subcellular locations in UniProt. The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which also includes membrane topology and orientation terms."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://www.uniprot.org/locations/"

Node: dcid:prositeID
typeOf: schema:Property
name: "prositeID"
description: "The identifier in PROSITE database. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."
rangeIncludes: schema:Text
domainIncludes:dcs:Antibody
descriptionUrl:"https://prosite.expasy.org/index.html"

Node: dcid:isPharmacokineticRelationship
name: "isPharmacokineticRelationship"
typeOf: schema:Property
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24 changes: 0 additions & 24 deletions biomedical_schema/chemical_compound_enum.mcf
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Expand Up @@ -2493,30 +2493,6 @@ name: "ProteinOccurrenceReliabilityUncertain"
description: "If the antibody-staining pattern contradicts experimental data or no expression is detected on the RNA level."
descriptionUrl: "https://www.proteinatlas.org/about/assays+annotation#if_reliability_score"

Node: dcid:AntibodyTypeEnum
typeOf: schema:Class
subClassOf: schema:Enumeration
name: "AntibodyTypeEnum"
description: "The antibody type enumeration which includes bispecific antibody, nanobody and DARPins."

Node: dcid:BispecificAntibody
typeOf: dcs:AntibodyTypeEnum
name: "BispecificAntibody"
description: "The term bispecific antibody (bsAb) is used to describe a large family of molecules designed to recognize two different epitopes or antigens."
descriptionUrl: "https://www.nature.com/articles/s41573-019-0028-1"

Node: dcid:NanobodyAntibody
typeOf: dcs:AntibodyTypeEnum
name: "NanobodyAntibody"
description: "A single-domain antibody (sdAb), also known as a nanobody, is an antibody fragment consisting of a single monomeric variable antibody domain."
descriptionUrl: "https://en.wikipedia.org/wiki/Single-domain_antibody"

Node: dcid:DarpinAntibody
typeOf: dcs:AntibodyTypeEnum
name: "DarpinAntibody "
description: "DARPins (an acronym for designed ankyrin repeat proteins) are genetically engineered antibody mimetic proteins typically exhibiting highly specific and high-affinity target protein binding."
descriptionUrl: "https://en.wikipedia.org/wiki/DARPin"

Node: dcid:RelationshipAssociationTypeEnum
typeOf: schema:Class
subClassOf: schema:Enumeration
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