. "Conferences in EasyChair"^^ . . "bgee@sib.swiss" . "https://sciflection.com/$1"^^ . "Contributor Role Ontology" . . . . . . . . "https://www.cbioportal.org/study/summary?id=$1"^^ . . "0007404"^^ . "Health Surveillance Ontology" . "false"^^ . "https://www.orthodb.org"^^ . . . . . . . . . . . . . "ENSG00000136147"^^ . . "obo" . "CA981206459"^^ . . . . . . "XB-GENE-922462"^^ . . . . . "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^ . . . . . "person" . "18125"^^ . . . . . . . "^\\d+$"^^ . . . . "Groundnut ontology" . "BEI_Resources" . . "An ontology to represent genomics cohort attributes."^^ . . . . . . . . "traumatology" . . "nlx" . . . . . . "translational medicine" . . . . . . "https://code.google.com/archive/p/ontology-for-genetic-interval/"^^ . "false"^^ . "cogs@ncbi.nlm.nih.gov" . . "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . . . "4019477"^^ . "false"^^ . . . . . . "false"^^ . . "International Classification of Diseases, 9th Revision" . . "^\\d+$"^^ . _:Na7345ed3b17d42ffa48b62644523a903 "Jeffrey A. Detras" . . . . "https://github.com/OGMS/ogms"^^ . "https://www.ebi.ac.uk/citexplore/"^^ . . "SwissLipid" . . . . . "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . . . . . "chemistry" . . . "interaction" . . "CVCL" . . . . . "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . . . . . . "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . . . . "http://www.yeastgenome.org/"^^ . "131392"^^ . . . . . "^\\d+$"^^ . . "Biological Collections Ontology" . . "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/"^^ . . . . . . "http://www.drugbank.ca"^^ . "H-InvDb Protein" . . . "subject agnostic" . . "genome" . . . "ebf69ca24298b28b2361e7d43eb52d6c"^^ . "^\\d+$"^^ . "^\\d+$"^^ . "https://github.com/MPIO-Developers/MPIO"^^ . "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1"^^ . "ComplexPortal" . . "^MMP\\d+.\\d+$"^^ . . . . . "ontology" . . . "false"^^ . "Gene"^^ . . . . . "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . "Antibiotic Resistance Ontology" . "SPIKE Map" . . . . . "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets"^^ . . . . . "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . . "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . . . . "obo" . . . "http://dictybase.org/"^^ . . "obo" . . . . . "false"^^ . . "0001191"^^ . "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . . . . . . . . . . . "NXPFA" . . . . . . . "Registry" . . "https://www.confident-conference.org/index.php/Event_Series:$1"^^ . . . "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1"^^ . "animal husbandry" . "anatomy" . . . . . "https://cls.shop/$1"^^ . "UniProtKB-KW" . . . . . "^\\d{7}$"^^ . . . . . "9606117"^^ . . "rna" . "false"^^ . "Adverse Event Reporting Ontology" . . . . . "clinvar.variation" . . "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . . . . "rscheuermann@jcvi.org" . "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships."^^ . "true"^^ . . . . . . "0000008"^^ . _:N307905d4ab6c4b1d9ea61114d952a881 . "An ontology built for representating the organizational components of trauma centers and trauma systems."^^ . . . "anatomy" . "Damion Dooley" . . "false"^^ . . . . "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . . "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"^^ . "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . . "false"^^ . . "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging"^^ . . . . . "Peroxibase" . "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^ . . "biomedical science" . . . . . "Animal Genome Pig QTL" . "BioProject" . . . "chemistry" . "small molecule" . . . . . "life science" . . . . . . . . . "genome" . . . "false"^^ . . "health science" . . "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies."^^ . "iNaturalist Place" . . "false"^^ . . "false"^^ . . . "4685"^^ . . . . "pathway" . . "CONSO00010"^^ . "protein" . . "Lentil ontology" . . "dr.sebastian.koehler@gmail.com" . "dsonensh@odu.edu" . "Provisional Cell Ontology" . "false"^^ . "https://github.com/ufbmi/geographical-entity-ontology/wiki"^^ . "ontology" . "drug metabolism" . . "^\\d+$"^^ . "identifier for a scientific journal, in the UniProt database"^^ . . . "false"^^ . . "obo" . "interaction" . "false"^^ . . . "0100002"^^ . "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . . . . . "true"^^ . . . . . "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia."^^ . "alpha.tom.kodamullil@scai.fraunhofer.de" . "antibodies" . . . "https://pav-ontology.github.io/pav/"^^ . . "false"^^ . . . . "UniProt Subcellular Locations" . "0100010"^^ . . "Protein covalent bond" . . . . "LINCS Cell" . . "CHEBI" . . . "life science" . "life science" . . . . "false"^^ . . . . . . . "http://ctdbase.org/"^^ . . . . . . . "http://cell-lines.toku-e.com"^^ . . . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . "ExAC Transcript" . . "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks."^^ . . . . "false"^^ . "obo" . . "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . . "https://github.com/obophenotype/ctenophore-ontology"^^ . . . . "Stemcell Knowledge and Information Portal" . . . . . . . . "aellenhicks@gmail.com" . "genome" . . "false"^^ . "https://rapdb.dna.affrc.go.jp/"^^ . "false"^^ . . "genetics" . "false"^^ . . . . "false"^^ . . "RIKEN Bioresource Center Cell Bank" . . . "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . . . . "ontology" . . . "Ximbio" . . . "https://bacteria.ensembl.org/id/$1"^^ . "Database for Prokaryotic Operons" . . . . . "^\\d{5}$"^^ . . . "false"^^ . . . "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . . "http://www.genome.jp/kegg/genes.html"^^ . . . . . . . . . . "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . "ontology" . . . "https://flowrepository.org/id/$1"^^ . . . _:N607bc2254b6340bca43002cca2cc3f1d "futo@stanford.edu" . "https://go.drugbank.com/categories"^^ . . . . "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . "miriam"^^ . . "m.a.laporte@cgiar.org" . . . . . . . . "obo" . "^[1-9][0-9]*$"^^ . . . "^\\d{6}$"^^ . . . "^\\d{7}$"^^ . . "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . "HIP000030660"^^ . . "http://www.hmdb.ca/metabolites/$1"^^ . . . "ICD" . "https://bdsc.indiana.edu/about/mission.html"^^ . . "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . . "ontology" . "Gianni Cesareni" . . . "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^ . . . . "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . . . . . "https://www.encodeproject.org"^^ . "Sequence types and features ontology" . . . . "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . . "https://dip.doe-mbi.ucla.edu/"^^ . "HIT000195363"^^ . "Mammalian Phenotype Ontology" . . . . . . "developmental biology" . . . . . _:N547f79cf887446f486241f7474b75009 "Patricia Brooks" . "^\\d{7}$"^^ . . . "chemistry" . "^\\d+$"^^ . "true"^^ . "false"^^ . . . "CHEBI" . . . . . . . . . . "https://bibliontology.com/"^^ . "http://purl.obolibrary.org/obo/PECO_$1"^^ . . . "ArrayGroup"^^ . "http://purl.obolibrary.org/obo/REO_$11"^^ . . . . . . . . . . . . . "^\\d{5}$"^^ . "gene" . . "^TA\\d+$"^^ . "plant breeding" . . "systems biology" . "obo" . "genomics" . . . "false"^^ . . "authorList"^^ . "egon.willighagen@maastrichtuniversity.nl" . "false"^^ . . . "hpiwowar@gmail.com" . "medical informatics" . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes."^^ . . . . "0000389"^^ . "^\\d+$"^^ . "Rosa2"^^ . . "http://www.mirbase.org/"^^ . "life science" . . "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . "617102"^^ . "^\\w+$"^^ . "bibliography" . "Google Scholar Researcher" . "https://www.xenbase.org/entry/$1"^^ . . . . . . . . . "MetaCyc" . _:N77939ae217a249ffaa546ae84afcdac5 . "http://www.cathdb.info"^^ . "molecular physical chemistry" . "false"^^ . . . "obo" . . "http://www.isni.org/isni/$1"^^ . "DICOM Controlled Terminology"^^ . . "0001350"^^ . _:Ncde5d2f3d7fb4e6cba489123361b62ca . . . "structure" . "Tribolium Genome Database -- Insertion" . "http://www.cba.ac.cn"^^ . . . . . . "NA06985"^^ . . . "Troy Pells" . . . . . . . . . "https://www.proteomicsdb.org/#peptideSearch"^^ . . . "pharmacology" . . "https://www.alzforum.org/mutations"^^ . . . "Bgee stage" . . . . "false"^^ . . . "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . "^\\d+$"^^ . . "0000001"^^ . "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . . "life science" . . . "http://www.wikigenes.org/"^^ . . "https://www.ebi.ac.uk/chembl/entity/$1"^^ . . . . "rna" . . "hydrogeology" . "gene" . . "agriculture" . . . . . . . "false"^^ . . . . . . "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . . . . "http://www.mgc.ac.cn/ShiBASE/"^^ . . "https://www.imanislife.com/?s=$1"^^ . . . . . . . "https://www.beiresources.org"^^ . . "http://neuinfo.org/"^^ . . _:N5454f1fae6264ca49a011d18d681fe28 "Crop Ontology Helpdesk" . . . "small molecule" . "Terry Hayamizu" . . "The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits."^^ . "false"^^ . . "^\\d+$"^^ . "Database of small human noncoding RNAs" . . _:N4213c5c2c69c424597c439c5a58c14a7 . . . _:Ndd2597b2adc04c7b85ebc82d11dfc398 . . "Assists in resolving data across cloud resources."^^ . "http://terminology.hl7.org/CodeSystem/v2-$1"^^ . . . . . . "AURKA"^^ . . . . "^\\d{7}$"^^ . . "false"^^ . "preclinical studies" . "false"^^ . "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . "3792"^^ . . . "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . "https://github.com/AnimalGenome/vertebrate-trait-ontology"^^ . "Arabidopsis Information Portal" . . "https://pictar.mdc-berlin.de/"^^ . "metabolites" . . "MetaNetX compartment" . . "true"^^ . . . . . . . . . "interaction" . "^\\d+$"^^ . . . . . "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . . . . . "https://sumlineknowledgebase.com/"^^ . "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge."^^ . . "biomedical science" . "bibliometrics" . "false"^^ . . "false"^^ . . . . "KEGG COMPOUND" . "^\\d+$"^^ . . . "http://purl.org/dc/terms/$1"^^ . "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . . . . . . "http://purl.obolibrary.org/obo/FYPO_$1"^^ . "^WBRNAi\\d{8}$"^^ . "Gene Normal Tissue Expression" . "aap-1"^^ . "false"^^ . . "ontology" . . . "CHEMBL4303805"^^ . "12"^^ . . "GR_PROTEIN" . . "http://purl.obolibrary.org/obo/MMO_$1"^^ . . . "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms."^^ . . . . "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^ . . . . . . "biodiversity" . . "^\\d{7}$"^^ . "protein" . "^\\d+$"^^ . . . "http://en.wikipedia.org/wiki/Main_Page"^^ . . . "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . . "false"^^ . . "NLXOEN" . "biomedical science" . "translational medicine" . . . . "https://github.com/"^^ . "depod@embl.de" . . . . "false"^^ . "SEED Compound" . . . "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary"^^ . "https://www.ebi.ac.uk/metagenomics/"^^ . . . . "^\\d+$"^^ . "false"^^ . "Nucleotide" . . . "false"^^ . "classification" . . . . . . . . "medicine" . . . . "0000004"^^ . "agriculture" . . . . "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources."^^ . "dna" . . . . . "http://www.radiomics.org/RO"^^ . "0778"^^ . . "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . . "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships."^^ . . "0000001"^^ . . "01467"^^ . "false"^^ . "tissue" . . . . "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^ . "false"^^ . . . . . "false"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . . "false"^^ . "Enzo Life Sciences is an antibody vendor."^^ . "dna" . . . . . "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . . . . . . "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . . . "proteomics" . . "http://genatlas.medecine.univ-paris5.fr/"^^ . "false"^^ . . . . . "^\\d+$"^^ . "1-55516888-G-GA"^^ . "false"^^ . "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . . "false"^^ . . "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . . . . "STOREDB at University of Cambridge" . "^\\d{7}$"^^ . . . . . "https://molmedb.upol.cz/mol/$1"^^ . "http://www.imdrf.org/"^^ . . . "200282"^^ . . "^\\d+$"^^ . . "https://flybrain-ndb.virtualflybrain.org"^^ . "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . "https://github.com/geneontology/go-ontology"^^ . "http://edamontology.org/format_$1"^^ . . . . "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . . _:N5454f1fae6264ca49a011d18d681fe28 "helpdesk@cropontology-curationtool.org" . "https://www.ebi.ac.uk/intact/search?query=$1"^^ . "SM0000020"^^ . . . "MOL000160"^^ . "ENSGT00550000074763"^^ . . . "GN_G03681DA"^^ . . "https://www.ccdc.cam.ac.uk/"^^ . . . . "false"^^ . "^\\d{7}$"^^ . . . . . . "^\\d{7}$"^^ . . . "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"^^ . "^PRJ[DEN][A-Z]\\d+$"^^ . "preclinical studies" . . . . "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . . . "SpBase" . . "false"^^ . . . "ALX-210-175"^^ . . _:N759fef0b0df5436c8989c13611dfe04d "alberto.traverso@maastro.nl" . . "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . . . "ENCSR163RYW"^^ . . . . . "http://www.antweb.org/"^^ . "0.7-123"^^ . . . "FAIRsharing Subject Ontology" . . . . "false"^^ . . "identifiers.namespace" . "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands."^^ . "data visualization" . . "https://ximbio.com/reagent/$1"^^ . . . . "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^ . . "virology" . . "http://microbialphenotypes.org"^^ . "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . . . . . . "go.chemicals" . "90806"^^ . . "false"^^ . "true"^^ . . . "protein" . . "https://progenetix.org/"^^ . . . . . . . "false"^^ . "anatomy" . "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR)."^^ . . "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . . . . "disease" . "Process Chemistry Ontology" . "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . . . . . "structure" . . . . "RiceNetDB miRNA" . . "http://purl.obolibrary.org/obo/TO_$1"^^ . . "false"^^ . . . . . . . "biology" . . . . "false"^^ . "Nathan Baker" . . "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . . . "^\\w+$"^^ . "cell lines" . . "Dictyostelium discoideum phenotype ontology" . . . "chemistry" . . "Name-to-Thing" . . . "FlyBase internal citation identifiers"^^ . "90062901"^^ . "https://www.brainspan.org/"^^ . . "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx"^^ . . . "ontology" . . "0003463"^^ . . . "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . "life science" . "false"^^ . "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . "http://www.oid-info.com/get/2.16.840.1.113883.6" . "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . . . . . . . "^\\d{7}$"^^ . . "https://neurovault.org/collections/$1"^^ . . . "structure" . "http://supfam.org/SUPERFAMILY/"^^ . . "NCBI PubChem database of bioassay records" . . . . . . "^\\d{7}$"^^ . "http://exac.broadinstitute.org/gene/$1"^^ . . . "false"^^ . . "http://geneontology.org/" . . . . "UMLS" . "ABE-0009634"^^ . . . "false"^^ . . "http://multicellds.org/MultiCellDB/$1"^^ . "false"^^ . "microbiology" . "false"^^ . . . "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . . "bioregistry"^^ . . "https://github.com/ewilderj/doap/wiki"^^ . . . . . "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . "0000021"^^ . "false"^^ . . . . "Gene Ontology Registry" . . . "OGI.owl" . "obo" . . . "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . . "life science" . "The international standard for identifying health measurements, observations, and documents."^^ . . "phylogenetics" . . . . "obo" . . . . . . "narcis.fernandez@gmail.com" . "https://proteinensemble.org/$1"^^ . . . . . . . . "false"^^ . . . . . "false"^^ . "organic molecular chemistry" . "Microbial Conditions Ontology is an ontology..."^^ . "http://code.google.com/p/mirna-ontology/"^^ . "spider" . . . . "315.1"^^ . . "ML0224"^^ . "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . . "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . . "0000205"^^ . . . "false"^^ . . . . . "true"^^ . "5fde96bdc5f1aa9ff0cce18a"^^ . . . . "false"^^ . "MTHICD9_2006" . . . . . . "plwhetzel@gmail.com" . . . . "false"^^ . . . . . . "bcp47" . "obo" . "stefan.kuhn@dmu.ac.uk" . . "^\\d{8}$"^^ . "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . "ontology" . . . "small molecule" . "analytical chemistry" . "obo" . "http://pepbank.mgh.harvard.edu/interactions/details/$1"^^ . . "biomedical science" . "https://gdc.cancer.gov"^^ . "mouse" . "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . . . "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^ . "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . . . . "241"^^ . . . "false"^^ . . "ACC-1"^^ . . . . . "S000002493"^^ . "molecular biology" . . . "https://rnacentral.org/rna/$1"^^ . "false"^^ . . . "Biotin_biosynthesis"^^ . . . . "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . . . "protein" . "Cell line databases/resources"^^ . . . . . "^\\d+$"^^ . . . "MycoBrowser smegmatis" . "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology"^^ . "^HBG\\d+$"^^ . . . "ontology" . . . "biochemistry" . . . "PdumDv" . . . . . . . . _:N8ab4ae8e36484efc953eb75de629f548 "chebi-help@ebi.ac.uk" . _:N76121237cb5847b48bb435c4bd4933ac . . . "liumeng94@sjtu.edu.cn" . . "ontology" . "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3"^^ . "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . . . "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . . "molecular microbiology" . "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression."^^ . "Guide to Pharmacology Ligand" . . . "Bilateria anatomy" . "false"^^ . . . "true"^^ . . "https://link.springer.com/bookseries/562"^^ . . . . . "^\\d+$"^^ . "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . . . "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . . . "DI" . . . . "genomics" . "https://eds.gene.le.ac.uk/home.php?select_db=$1"^^ . "00573"^^ . . . "DASHR expression" . . "^\\d+$"^^ . . "Gene Expression Ontology" . . "Lin Huang" . . . . . . "janna.hastings@gmail.com" . "Cell line collections"^^ . "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . . "https://www.nlm.nih.gov/research/umls"^^ . . "CIViC Disease" . . . . . "rna" . "CY077097"^^ . . "1915"^^ . "T06648"^^ . . . . . . "Mingxun Wang" . . . . . "S7000002168151102"^^ . . . "1968"^^ . . "false"^^ . . "^\\d{7}$"^^ . "https://cropontology.org/rdf/CO_343:$1"^^ . . "false"^^ . "wujm@bjmu.edu.cn" . . "Clair Kronk" . . "An application ontology for use with miRNA databases."^^ . . . . . "http://purl.obolibrary.org/obo/ATO_$1"^^ . "Ensembl Gene" . . . . . "BacMap Biography" . "false"^^ . . . . . . . . "http://purl.obolibrary.org/obo/AERO_$1"^^ . "Linear double stranded DNA sequences" . "https://cropontology.org/rdf/CO_336:$1"^^ . . . "http://mampol.uab.es"^^ . "^\\d{5}$"^^ . "https://aopwiki.org/"^^ . "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . . . "http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry"^^ . _:N1e9ea2c4b81042489082f71ead4a643c "dylan.mcgagh@magd.ox.ac.uk" . . "false"^^ . . . . "^\\d{1,5}$"^^ . . . . . "^[0-9]+$"^^ . . . . . "Diseases Database" . . "https://www.w3.org/TR/xml/"^^ . . . . . . "^HIP\\d{9}(\\.\\d+)?$"^^ . "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . . "A controlled vocabulary to support the study of transcription in the primate brain"^^ . . "^\\d+$"^^ . . . . . "protein" . . . . . . . . "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . . "cpga" . . "^.+$"^^ . "9"^^ . . . . . "false"^^ . "false"^^ . "ontology" . "structure" . . . "jason.stajich@ucr.edu" . . . . . . . . . "ontology" . . . . . . "288"^^ . "Ontology of standardized units"^^ . "https://www.omim.org/phenotypicSeriesTitles/all"^^ . "false"^^ . "preclinical studies" . "addiehl@buffalo.edu" . "obo" . . . . . "RNA Modification Database" . . . . "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^ . . . . . . "An anatomical and developmental ontology for cephalopods"^^ . . "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . "^ENSGT\\d+$"^^ . . . . . . "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . "https://www.kegg.jp/entry/$1"^^ . . . . . "false"^^ . . "false"^^ . . . . . "^DBCAT\\d+$"^^ . "^\\d+$"^^ . . . . "http://www.membranetransport.org"^^ . . . . "https://www.reaxys.com"^^ . _:N99a15b5463404fb0a2bd56a69fd28b6a . "https://github.com/ApolloDev/apollo-sv"^^ . "PTHR12345"^^ . . . . . . "protein" . . "PathBank" . "Enzo Life Sciences" . . "http://probonto.org"^^ . "false"^^ . . . "protein" . _:N5a03ce082bca497386cde242e72b4108 "bakerc@unb.ca" . "botany" . . "^[A-Za-z 0-9]+$"^^ . . "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . "gene expression" . "obo" . . . . . "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . . . "http://doqcs.ncbs.res.in/"^^ . "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . . . . . "false"^^ . . . . "false"^^ . "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . . . . . . "https://www.ncbi.nlm.nih.gov/nlmcatalog"^^ . . . . . . . "Jesualdo Tomás Fernández-Breis" . . "proteomics" . . "^ENSG\\d{11}$"^^ . . . . . . . "https://github.com/rsc-ontologies/rxno"^^ . . . "structure" . "life science" . . . "http://tumor.informatics.jax.org"^^ . . . . . . . "biology" . "http://www.semantic-systems-biology.org/apo"^^ . "MedDRA" . "00000001"^^ . . "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . . "The Behaviour Change Intervention Ontology" . . "Allotrope Merged Ontology Suite"^^ . . . . . _:N18ba8036031444908430f52cf74e7537 "helpdesk@cropontology-curationtool.org" . . . "false"^^ . . . . . "life sciences" . "rdb20@pitt.edu" . "http://zinc15.docking.org/substances/$1"^^ . "dna" . . "false"^^ . . "CHEBI" . . . . . . . . "medicine" . . "ontology" . . . "https://www.pirbright.ac.uk/tick-cell-lines-views-page"^^ . . . "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . "NIF Standard Ontology: Digital Resources" . "https://athena.ohdsi.org/search-terms/terms/$1"^^ . . . . . . . . . "https://www.gbif.org/species"^^ . . . . . "^PR\\d{5}$"^^ . . _:N9f748acc83f4497888553bf5e7fab3f7 "Vladimir Mironov" . . . . . "https://mmp.sfb.uit.no/databases/marfun"^^ . "hsa-let-7a"^^ . . "UP000005640"^^ . . . _:Ndca238f5dfd5446993329dbd1696e8f6 . "false"^^ . "http://addgene.org/$1"^^ . "34"^^ . "fly" . "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . "Banco de Celulas do Rio de Janeiro" . . . . . "huanglin36@mail.sysu.edu.cn" . . . "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . . . . . "^MMP\\d+.\\d+$"^^ . "614"^^ . "ShareLoc" . . . . "metabolomics" . "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv"^^ . . . . . . "false"^^ . . "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . . "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse)."^^ . . "https://flybase.org/reports/FBtc$1"^^ . . "ClinicalTrials.gov ID" . "jupp@ebi.ac.uk" . . "false"^^ . . . "^\\d{7}$"^^ . . "https://proteininformationresource.org/resid/"^^ . "false"^^ . . "27267"^^ . "https://www.eurofir.org"^^ . . . "http://edamontology.org"^^ . . . . "protein" . "Human Brain Atlas" . "phenotype" . . . . . . "http://dictybase.org"^^ . . "false"^^ . . . "Vertebrate Genome Annotation Database" . . "enzyme" . . "http://exac.broadinstitute.org/variant/$1"^^ . "biology" . . . . _:Ncde5d2f3d7fb4e6cba489123361b62ca "Crop Ontology Helpdesk" . "false"^^ . "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation."^^ . . . . . "anatomy" . "^\\d+$"^^ . . . . . . . . . "^\\d{7}$"^^ . . "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . "https://www.ncbi.nlm.nih.gov/PubMed/"^^ . "http://www.ebi.ac.uk/efo/EFO_$1"^^ . . "Search the world's most comprehensive index of full-text books."^^ . . "MU9_3181"^^ . . "Activity Streams" . . . . "https://civicdb.org/"^^ . . . . "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . . . "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."^^ . . "PXD000500"^^ . . "obo" . . "The Arabidopsis Information Resource" . "life sciences" . . . . . . "https://github.com/aszool/oarcs"^^ . "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . . "RNAloops" . . . . . "The SEED;" . . . . "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . . . . "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . . "^\\d{7}$"^^ . . . "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . . . . "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . . . . . . "SYMP" . "false"^^ . "interaction" . . . . "https://genome.ucsc.edu/"^^ . "small molecule" . . . . . . . . "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . "Database of Genomic Structural Variation - Study" . "^\\d+$"^^ . . "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . . "life science" . . . . . . "^\\d{7}$"^^ . . . . . "genes" . . "taxonomy" . . "Variants in dbVar."^^ . "https://github.com/obophenotype/c-elegans-development-ontology"^^ . "false"^^ . . . . . . "false"^^ . . . "data management" . . "ontology and terminology" . "277.9"^^ . . "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^ . . . "false"^^ . "https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data"^^ . . "cognitive neuroscience" . . . . . "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . . . . "Datanator Reaction" . "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . . . . "false"^^ . . . . "^\\d+$"^^ . . . "^[A-Z0-9]{5}\\d+$"^^ . . . . . "Meng LIU" . . . "https://tools.ietf.org/rfc/rfc$1"^^ . "https://cropontology.org/ontology/CO_340/Cowpea"^^ . . . . . . "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1"^^ . . "https://cropontology.org/ontology/CO_321/Wheat"^^ . . . . "life science" . "^\\d{7}$"^^ . "^m\\w+$"^^ . . . . . . "gene" . . . . . "https://www.biozol.de/en/product/$1"^^ . . "http://www.antirrhinum.net/"^^ . . "PIRSF000100"^^ . . "small molecule" . "sequence" . . . . . "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment."^^ . . . . . . . . "http://edamontology.org/topic_$1"^^ . . . . "https://prefix.cc/" . . "434"^^ . . . . . "molecular infection biology" . "vertebrate" . "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . _:N0ff60f4fd7de40d98aa4b920f35763dc "Sheeba Samuel" . "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . . "false"^^ . "^[A-Za-z0-9-]+$"^^ . . . . "http://modelseed.org/"^^ . "wdduncan@gmail.com" . "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$"^^ . "Assembly" . . "ontology" . "HDAA2" . "false"^^ . "false"^^ . . . . . . . . "Alzheimer's Disease Ontology" . "http://scop.mrc-lmb.cam.ac.uk/scop/"^^ . . "http://www.w3.org/ns/shex#"^^ . "16793"^^ . "UniProt Chain" . . "glycosciences.db" . . "false"^^ . _:N683f622c282e492a86e4f82b7c2707f9 . "https://github.com/micheldumontier/semanticscience"^^ . . . "http://www.jstor.org/stable/$1"^^ . . . "http://www.sanger.ac.uk/Users/mb4/PLO/"^^ . . "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . . "090701"^^ . . "^\\d+$"^^ . . . "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . . . "^CHEMBL\\d+$"^^ . . "http://www.cathdb.info/cathnode/$1"^^ . . "gomfid" . "obo" . "DrugBank Salts" . "GLDS-141"^^ . "life science" . "Variable"^^ . . "http://genecards.weizmann.ac.il/genenote/"^^ . "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1"^^ . . . . "SNOMEDCT_2005_07_31" . "^\\d+$"^^ . . . "ontology" . . . . . _:N3a04b532445341fd8e4e60bc5c463d6c . "genomics" . . . "life science" . . . . . . _:Ncbb9b62ced6245bcbdec488b0d39f614 . . . . . . "Mouse Developmental Anatomy Ontology" . . "ontology" . . "00005643"^^ . "systems biology" . . "0000187"^^ . . . . . . . "https://www.itis.gov/"^^ . "Ion Channel Electrophysiology Ontology" . . . "HMDB" . "false"^^ . . . . . . . . . _:N3d370edf9f7a448e845737d212ddee90 "BioModels.net team" . . "Molecular Process Ontology" . . . . . "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . "ontology" . . . . . . "https://signor.uniroma2.it"^^ . . . . "A subspace of Metabolic Atlas for reactions."^^ . . "false"^^ . . . . . "Ontology of Biological Attributes" . "false"^^ . . "^\\w+$"^^ . _:Nbfdd010fa12a4eeeb3209d833cec0ed1 . . . "10595"^^ . . . . "false"^^ . . . "https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1"^^ . "Research Organization Registry" . "http://ecogene.org/"^^ . . . "Pol Castellano Escuder" . . "false"^^ . . . . . . . "false"^^ . . "false"^^ . "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . . . . "microbiology" . "^\\d{7}$"^^ . "developmental biology" . . . . . . . . _:Nf361fabd216b4e09adf724fed0a47670 "Stephan Schurer" . . "biomedical science" . "^\\d{7}$"^^ . . . "0400109"^^ . . "^\\d{7}$"^^ . . . . "merops.inhibitor" . "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA."^^ . . . . . "omics" . "http://www.uniprot.org"^^ . "true"^^ . . "life science" . . "http://www.cathdb.info/"^^ . . . . "ZFA_RETIRED" . . . "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'."^^ . . "https://www.inaturalist.org/places"^^ . . . . . "false"^^ . "http://purl.obolibrary.org/obo/DINTO_$1"^^ . . . . . "false"^^ . "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . . "http://purl.obolibrary.org/obo/CARO_$1"^^ . . "Chinese Biological Abstracts" . . "http://www.drugtargetontology.org/dto/DTO_$1"^^ . "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd"^^ . . "^\\d{7}$"^^ . . . "social science" . . "microbiology" . . . "Current Procedural Terminology" . . . "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . . "false"^^ . . . "false"^^ . . . . . . . "false"^^ . . . . . . "^\\d{7}$"^^ . . . . . "false"^^ . "silvio.peroni@unibo.it" . . . "ontology" . . . . "http://bacmap.wishartlab.com/organisms/$1"^^ . . . . "^\\w+$"^^ . . . . "evolutionary biology" . "K00973"^^ . . . . . . . "WoRMS-ID for taxa" . . "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . . . "Tick Cell Biobank" . "ontology" . . "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^ . . "D0001"^^ . "Yongqun Oliver He" . _:N1c71142892be44b68b04c73f72b70088 "mejino@u.washington.edu" . . "AURKA"^^ . . "Resources mentioned in \"Sharing biological data: why, when, and how\"" . "https://pharmacodb.ca/cell_lines/$1"^^ . "LinkML" . "genomics" . . . . . . . . "agriculture" . "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . . . "gene" . . "false"^^ . . "http://purl.obolibrary.org/obo/MOP_$1"^^ . . "achcar11"^^ . . "gene" . "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . . . "TAIR Protein" . . . . "0000609"^^ . "metabolite" . "^\\d+$"^^ . . . "clustering" . . "OMA Group" . "^\\d{6}$"^^ . "ppdb@gifu-u.ac.jp" . . . . . "dna" . "1"^^ . "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . "19210-3"^^ . . . . "Proteomics data and process provenance" . "http://purl.obolibrary.org/obo/TAHE_$1"^^ . . . "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . . "eggNOG" . "http://www.massbank.jp"^^ . . . . "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data."^^ . "true"^^ . . . "ACM1_HUMAN"^^ . "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . "Terms from the source appear in the target resource" . . . "http://vbrc.org/"^^ . . . . "false"^^ . "global health" . "Porifera Ontology" . "BN000065"^^ . . . . . "https://fairsharing.org/"^^ . . "http://www.ymdb.ca"^^ . "Homology Ontology" . . "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^ . . . "ontology" . . . . . "MGYA00002270"^^ . "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . "https://www.wormbase.org/db/seq/protein?name=$1"^^ . . . "BiGG Compartment" . "Nonribosomal Peptides Database" . . . . "obo" . . "^rs\\d+$"^^ . . . . . "OriDB Saccharomyces" . . . . "http://elm.eu.org/"^^ . "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . . "ontology" . . . . "1000100"^^ . . . . . . . "MarDB" . . . "638309541"^^ . . . . . . . . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . "https://github.com/proco-ontology/PROCO"^^ . . . . . "NAD%20biosynthesis"^^ . . . . . . . . . . "CALIPHO Group Ontology of Human Anatomy" . . "paolo.romano@hsanmartino.it" . . . . . . . . . . . "Identifier of a taxon or synonym in the Catalogue of Life"^^ . "https://www.inaturalist.org/observations"^^ . . "obo" . . . . "neurophysiology" . "life science" . "Datanator Metabolite" . "subject agnostic" . . "^\\d+$"^^ . "US4145692"^^ . . . . "Teleost taxonomy ontology" . "c0001"^^ . "https://www.grid.ac/"^^ . "pns12@hermes.cam.ac.uk" . . . . . "ontology" . "genetics" . "Europe PMC Preprints" . . "https://github.com/EBISPOT/amphx_ontology"^^ . . . "false"^^ . . "https://github.com/$1"^^ . . "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . "virology" . "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . . "^\\d{7}$"^^ . . "https://mapping-commons.github.io/semantic-mapping-vocabulary/"^^ . "https://www.sharkipedia.org/"^^ . . "Telethon Network of Genetic Biobanks" . . . "enzyme" . . . . . "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^ . "life science" . "0000000"^^ . . . . . "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . . . . . "http://spbase.org"^^ . "https://www.addexbio.com/productdetail?pid=$1"^^ . . . "Sierra Moxon" . . . . . "Drug Central" . "^\\d+$"^^ . "0000504"^^ . "comparative genomics" . "3639"^^ . . "false"^^ . . . . . "batchelorc@rsc.org" . "http://www.receptome.org"^^ . "5601141"^^ . "634515043"^^ . . "0002999"^^ . . . . . . . . . . "KEGG Reaction Class" . "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . . "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^ . "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . "life science" . . "karel.berka@upol.cz" . "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . . . _:Nff3f5dc527c943b3835b7e766ad31d06 . . "NIF Standard Ontology: Brain Regions" . . . . "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"^^ . . "ontology" . . . . . . "Platynereis stage ontology" . "^[\\w\\-.]{3,}$"^^ . . . . . . . . . "^\\d{7}$"^^ . . . "https://terminology.hl7.org/codesystems-v2.html"^^ . "structure" . "anatomy" . . . "CAL0003079"^^ . . . . "Medical Action Ontology" . . "Sol Genomics Network" . "primary health care" . . . . "The reviewer of a prefix" . . "ontology" . . . "genome" . . . "obo" . "^\\d+$"^^ . . . _:N41fc52bc74b747e0abb726794638628f "yingqin@rti.org" . . . "anatomy" . "zebrafish" . . . "cytology" . . "^\\d{7}$"^^ . "Unified Phenotype Ontology" . . . "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . "life science" . . . . "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . . . "false"^^ . "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"^^ . . "HGVPM623"^^ . . . "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design."^^ . "SM_UB-81"^^ . . "plasmid" . "gene expression" . . . . . . . . . "rsk00410"^^ . . . . . "https://www.cellbiolabs.com"^^ . . . "enzymology" . _:Nf15c3090109a4640b1a313455cc11170 "Crop Ontology Helpdesk" . "medicinal chemistry" . "ontology" . . . "https://winter.group.shef.ac.uk/molbase/"^^ . "https://identifiers.org" . . "false"^^ . . . . . . . . . . "Allergome" . . . . . . "0000001"^^ . "Cryo Electron Microscopy ontology" . . "307"^^ . "Heidi L. Rehm" . . "Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project." . . "^\\d{7}$"^^ . . . . . . "^\\d+$"^^ . . . . "genetics" . "false"^^ . "0000000"^^ . "dna" . . "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . . _:Nd4f08d3515444c528d8a102d1009303f "Plant Ontology Administrators" . "botany" . _:Nd3379fddb329489791db2fcef717a56f "Stephen Larson" . . "BEI Resources" . . . . "ChEBI Data Sources" . . "^[1-9]\\d*$"^^ . . . . . . . "relations" . "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^ . . "protein" . "genetics" . "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . . . . . . "The coding sequence or protein identifiers as maintained in INSDC."^^ . . "ontology" . . "https://stemcells.nindsgenetics.org?line=$1"^^ . "protein" . . . . . . . "true"^^ . . "^\\d+$"^^ . "pathway" . . . "4005"^^ . . . . "false"^^ . . . . . "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . . . . . . . . . . "http://www.aspgd.org/"^^ . . . . . . . . "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . "nucleotide" . "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI)."^^ . "glycomics" . . "subject agnostic" . . . . "Leafsnap ID" . . . . . . "^[a-z0-9\\-]+$"^^ . . "EY223054.1"^^ . . "false"^^ . . . "https://cropontology.org/rdf/CO_326:$1"^^ . . . "true"^^ . "chemistry" . "comparative genomics" . "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^ . . . . . "http://www.genome.jp/kegg/brite.html"^^ . . . . . . . . . "genomics" . "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones."^^ . "http://opencitations.net"^^ . "obo" . . "5277619"^^ . . "ontology" . "medicinal chemistry" . _:N6a97b0a899c04140b39f8f866227146f "po-discuss@plantontology.org" . "Andreas Ruepp" . . "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . . . "https://www.sharkipedia.org/"^^ . "https://run.biosimulations.org/simulations/$1"^^ . "eNanoMapper Ontology" . . . . . . . "KEGG_RCLASS" . "^CCDS\\d+\\.\\d+$"^^ . "fdb8a927-45c3-48b7-9743-cbb5e16837fa"^^ . . . "1"^^ . . "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type."^^ . "ontology" . "creeas@gmail.com" . "NCBIGene" . . "http://www.w3.org/2003/11/swrl#$1"^^ . . . "structural bioinformatics" . . "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . "https://www.brenda-enzymes.de/ligand.php"^^ . "1000"^^ . . "false"^^ . "feature"^^ . "Phy000CLXM_RAT"^^ . "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . "pathways" . "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records."^^ . "rna" . . . . "semantic web" . . . _:N588bd994c8224d689ed23febd19235cc "helpdesk@cropontology-curationtool.org" . "^\\d{7}$"^^ . . . . "neurobiology" . . . . . "http://paleodb.org/"^^ . . . "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . . "Sharkipedia Trend" . . . . "false"^^ . . "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . "NLXCELL conatins cell types with a focus on neuron types."^^ . "0001000"^^ . . "life science" . . . "agriculture" . "2679240"^^ . . . . . . "ISBN-13" . "2GC4"^^ . "57-27-2"^^ . "UCR00513"^^ . "bioinformatics" . . "life science" . . . "GCA_000155495.1"^^ . . . . "plant" . . "ABC"^^ . . . "http://purl.obolibrary.org/obo/PDRO_$1"^^ . "^TIGR\\d+$"^^ . "Michelle Giglio" . "http://sideeffects.embl.de/drugs/$1"^^ . "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^ . . . "computer science" . . "life science" . . . . "Google Books" . . _:Ne51bf5ccdd80474dad1322f9a5cf8b49 "michael.lincoln@va.gov" . . "natural science" . "WB_REF" . "http://ciliate.org/index.php/feature/details/$1"^^ . "OrthoDB" . "https://pubchem.ncbi.nlm.nih.gov"^^ . "Mechanism, Annotation and Classification in Enzymes" . "Selventa Diseases" . . . "http://eugenes.org:7072/.bin/fbidq.html?$1"^^ . . . . . "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . "obo" . . . "computational biology" . "DB14938"^^ . . . "0000013"^^ . _:N77723c2c96484f94a77a04510f99476a "Elspeth Bruford" . . . . . . "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . . . . . "NCit" . "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n"^^ . "false"^^ . . "botany" . "https://www.enzyme-database.org/"^^ . . "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . "metabolite" . "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . "LO362836C"^^ . "https://www.metabolome-express.org/"^^ . . . . . . . "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . . . "false"^^ . . "Japan Consortium for Glycobiology and Glycotechnology Database" . . "^GPST[0-9]{6}$"^^ . . "gene" . "pharmacogenomics" . "A set of guides on implementing various processes within hospitals or healthcare systems."^^ . . . . . . . "false"^^ . . "https://herv.img.cas.cz/s/$1"^^ . . . "Metabolic Atlas Reaction" . . . . . . "false"^^ . . . . . . . . . . . "life science" . . . . . . "^[1-9]\\d*$"^^ . . "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1"^^ . . "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^ . "https://gensc.org/mixs/"^^ . "true"^^ . . . . "obo" . . . . . . "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . . "https://comptox.epa.gov/dashboard"^^ . . . . . "transcript" . "biomedical science" . . . "WP732"^^ . "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . . "true"^^ . . . . . . . . "^\\d+$"^^ . . . "101775319"^^ . . . "SciCrunch Registry" . . . "smp-m3w9hbe"^^ . "The cell line vocabulary inside FlyBase"^^ . . . . "NodeShape"^^ . "http://asap.ahabs.wisc.edu/asap/home.php"^^ . "0000029"^^ . . . . . . "^\\d{7}$"^^ . "82"^^ . . . "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^ . "obo" . . . . "life sciences" . . . . . . . "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . "Meghan Balk" . . . . "epigenomics" . . . . "subject agnostic" . . "reagents" . . . . "false"^^ . . "true"^^ . . . . . . . "false"^^ . "environmental science" . . . . . . "The Food Ontology" . "Mosquito insecticide resistance" . . . . "G. Thomas Hayman" . . "https://rfam.xfam.org/"^^ . . "GenPept" . "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database."^^ . . . "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . . . . "http://oid-info.com/get/$1"^^ . "EG10173"^^ . . . . "obo" . "false"^^ . "0000050"^^ . . "MAM01234c"^^ . "ordo" . . . . "r3d100010772"^^ . . "https://www.re3data.org/repository/$1"^^ . . . "life science" . "life science" . "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . . "EasyChair Call for Paper" . "gene expression" . . "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . . . . . _:N6882598d78974fe4bfa7854a20ab8251 "WikiData Support" . . . . . . . "false"^^ . . "https://github.com/SciCrunch/NIF-Ontology"^^ . "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^ . . "https://www.animalgenome.org/QTLdb"^^ . "rna" . "^MMP\\d+.\\d+$"^^ . "https://www.ncbi.nlm.nih.gov/"^^ . "protein" . . . "false"^^ . . "National Library of Medicine Catalog" . "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^ . . . "regulation" . . . . "false"^^ . . "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . . . . . . . "https://github.com/OPMI/opmi"^^ . "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data."^^ . . . . . "^[a-zA-Z0-9_\\.]+$"^^ . . . "physiology" . . . "false"^^ . . . . . . . "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^ . . "https://pathbank.org/view/$1"^^ . "orchard@ebi.ac.uk" . . "alayne.cuzick@rothamsted.ac.uk" . . . "agriculture" . . "preclinical studies" . . "Dimension"^^ . . . . . "Molecule role (INOH Protein name/family name ontology)" . . "http://www.sparontologies.net/ontologies/fivestars"^^ . "http://purl.obolibrary.org/obo/COVOC_$1"^^ . "^\\d{4,6}$"^^ . "sequence" . . . . . "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . "false"^^ . . "0000254"^^ . . . "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:$1"^^ . "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^ . . "3000887619"^^ . "obo" . . . . . . "https://n2t.net/$1:"^^ . . "false"^^ . . . . . . "false"^^ . "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical ID" . . . . "environmental science" . . . . . . . . . . "false"^^ . "obo" . . . "support@bel.bio" . . . . . "false"^^ . . . "0000001"^^ . "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . . . "GFAM" . "NIFSTD" . . . . . . "https://books.google.com/books?id=$1"^^ . . . . . . . "https://cropontology.org/rdf/CO_359:$1"^^ . "biomedical science" . . . "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . "http://trace.ddbj.nig.ac.jp/bioproject/"^^ . . . . . "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . . . . . . . . "ScerTF" . . "Coconut ontology" . . . . . . "PK-DB" . . . . . "REBASE Enzyme Number" . . . "computational neuroscience" . . . . . . . . . "uniprot.db" . . . "https://drugs.ncats.io/drug/$1"^^ . . . "false"^^ . "http://www.t3db.org/"^^ . "http://viaf.org/viaf/$1"^^ . . . "life science" . . "Dataset"^^ . . . . "epidemiology" . "ontology" . "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . . "false"^^ . "obo" . "TTDS00056"^^ . . "false"^^ . . "conferences" . . "http://purl.obolibrary.org/obo/fbbt"^^ . "Platynereis Developmental Stages" . . . . . "anatomy" . "Citation Typing Ontology" . . . "^\\d+$"^^ . . . . . . "biopesticides" . . . . "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^ . . . "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . . . . . . . "ontology" . . "false"^^ . . . "^\\d+$"^^ . . . . "false"^^ . . "21877"^^ . . . "gomf" . "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration."^^ . "obo" . "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . . . . "http://purl.obolibrary.org/obo/DUO_$1"^^ . . . . . . . . "Affymetrix Probeset" . . . . . "100101"^^ . . . "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/"^^ . . . "UniProt Protein" . "http://purl.org/cerif/frapo/$1"^^ . "dhowe@zfin.org" . . . . "^\\d+$"^^ . "life science" . . . "false"^^ . . . . "4145692"^^ . "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place."^^ . . "http://purl.obolibrary.org/obo/OAE_$1"^^ . "https://github.com/IEDB/MRO"^^ . "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1"^^ . . "^(\\d{8}|(\\w+\\d+\\w+))$"^^ . "Tom Gillespie" . . _:Nf361fabd216b4e09adf724fed0a47670 . . "https://www.confident-conference.org/index.php/Category:Event_Series"^^ . . . "info@casrai.org" . . . . . "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts."^^ . . . . "^\\d{7}$"^^ . "^\\d{3}\\.\\d{2}$"^^ . . "^PA\\d+$"^^ . . . . . . . . . . . . . "subject agnostic" . . . . . . . . "Legacy site for IETF RFC proposals"^^ . . . . . . "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . "^[A-Z]{1,2}\\d{5}$"^^ . . "http://purl.obolibrary.org/obo/ARO_$1"^^ . . . . . "cheminformatics" . . . . . "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . . "UM-BBD_ruleID" . . "https://www.ebi.ac.uk/metagenomics"^^ . . . . . . "siiraa@umich.edu" . "true"^^ . "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . . . . . "^(data|topic|operation|format)\\_\\d{4}$"^^ . "phenomics" . . . . "CHEMBL3307800"^^ . . "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . . . "Rosemary Shrestha" . "genome" . "Human Oral Microbiome Database" . . . "Erik Segerdell" . . . . "genome" . _:N40c55e16a1204a5b98fc3ab54706d65f . "RCSB_PDB" . . . . "Disease Drivers Ontology" . . "preclinical studies" . . . "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information."^^ . "https://repeatsdb.org/structure/$1"^^ . . "17503"^^ . "https://polbase.neb.com/polymerases/$1#sequences"^^ . . "false"^^ . _:Ne51bf5ccdd80474dad1322f9a5cf8b49 "Michael J. Lincoln MD" . "^MTBLS\\d+$"^^ . . "^\\d+$"^^ . . . . . . "plant genetics" . . _:N588bd994c8224d689ed23febd19235cc . "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . . "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . . . "nsv3875336"^^ . "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . "0000088"^^ . . "^C\\d+$"^^ . "1001"^^ . "false"^^ . . "http://opendata.inra.fr/ATOL/ATOL_$1"^^ . "false"^^ . . . . . . "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . "http://purl.obolibrary.org/obo/CDNO_$1"^^ . "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . "^[0-9]+$"^^ . "Close to 5K Categorizations for drugs, similar to ATCC."^^ . "mutations" . "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . "Infectious Disease Ontology" . . "http://sugarbind.expasy.org/"^^ . "http://thebiogrid.org/$1"^^ . . . "ModelDB" . . . . "EGAS00000000001"^^ . . . . . . "http://ontoneo.com"^^ . "http://open-services.net/ns/core#$1"^^ . . "https://github.com/obophenotype/sibo"^^ . . _:N286ebf045f1c43cfade97ccb27c0227f "Jonathan Bard" . . . "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . . "ontology" . "Saccharomyces cerevisiae promoter database" . "taxonomy" . "false"^^ . . "ENSG00000026508"^^ . "Selventa legacy complex namespace used with the Biological Expression Language"^^ . . . "subject agnostic" . . . "http://www.ars-grin.gov/"^^ . . . . . . "ontology" . . "interaction" . _:Nfe920b0be73f431b87bc36150db824b5 "jamsden@us.ibm.com" . . "structrual bioinformatics" . "Narcis Fernandez-Fuentes" . . . . . . . "http://purl.org/spar/bido/$1"^^ . "botany" . . "MSBNK-IPB_Halle-PB000166"^^ . . . "Salk Institute for Biological Studies" . "^\\d+$"^^ . . . . "false"^^ . "Ontology of rat strains"^^ . . "obo" . . . . . "false"^^ . . . . . . "genomics" . "HIX0004394"^^ . "http://omia.angis.org.au/"^^ . . . . "Saccharomyces Genome Database" . . "genome" . . "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . "https://www.merckmillipore.com/catalogue/item/$1"^^ . . "^AT\\d+$"^^ . . . "14"^^ . "SRS086444"^^ . "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . . . "false"^^ . . "pain medicine" . "Expression"^^ . . "life science" . "Charles Tapley Hoyt" . . "false"^^ . . "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . "pathway" . . . "iNaturalist Observation" . . "https://depmap.org/portal"^^ . "neurophysiology" . . "IUPHAR_LIGAND_ID" . "epidemiology" . . . . . . "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . "0005452"^^ . . . . . . "^\\d{7}$"^^ . "https://morpheus.gitlab.io/"^^ . "false"^^ . . . "TGME49_053730"^^ . . . "intenz" . . . "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . . . . . "Morpheus model repository" . . . "life science" . . . . "Cell line collections"^^ . . . . "troy_pells@yahoo.ca" . "OMIM Phenotypic Series" . . "https://vega.archive.ensembl.org/index.html"^^ . . "ontology and terminology" . "gene" . . . . "4D Nucleome Data Portal Experiment Replicate" . . "http://search.sisuproject.fi/#/variant/$1"^^ . . "https://rism.digital/"^^ . "^\\d{7}$"^^ . "SECONDARY_CAS_RN" . . . "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^ . . . . "ndf-rt" . "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . . . . . . . "ECMDB" . . . . "life science" . . . . . . . . . "https://bioportal.bioontology.org/ontologies/NPO"^^ . "171"^^ . . . "biology" . "Shorthand representations of languages and their subtypes"^^ . . . "0000019"^^ . . "structure" . "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^ . . "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . . . . . . . . . . "true"^^ . _:Naa829a3066ad433c82f7b4472eb0a57f "vlee@ebi.ac.uk" . . . "chemistry" . . . "r.court@ed.ac.uk" . . "0000435"^^ . . . . . "ontology" . "^\\d+$"^^ . . . . "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^ . "http://purl.obolibrary.org/obo/MPIO_$1"^^ . . . "false"^^ . . . . "metagenomics" . "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . . . . "FBbt_root" . "life science" . "^NX_\\w+$"^^ . . . "obo" . . . "false"^^ . . . "Cell line collections"^^ . . "https://sciformation.com/sciflection.html"^^ . . "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . . "2c6s"^^ . "An ontology to capture confidence information about annotations."^^ . . . "obo" . "HUMAN16963"^^ . . . "anne.morgat@sib.swiss" . . . . . . . "146421"^^ . . "global health" . . . . "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). "^^ . "https://www.diseasesdatabase.com/ddb$1.htm"^^ . . "CTD Disease" . . "A0001"^^ . . . . . . "WikiGenes" . . "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . "false"^^ . "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . . . . . . . . "r3d100010772" . . . . . . . . "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . "Tetrahymena Genome Database" . "http://www.animaldiversity.org"^^ . . "false"^^ . . "PharmacoDB Tissues" . . . . . . "https://doi.org/$1"^^ . "^\\d{9}$"^^ . . . . . "false"^^ . . . "MEDLINE" . "The set of prefixes used in the Cellosaurus resource" . . . . "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"^^ . . . "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . . "false"^^ . "^\\w+$"^^ . "obo" . "^\\d+$"^^ . . . "obo" . . . . "0221"^^ . "^\\d+$"^^ . . "false"^^ . . . . . . "sequence" . . . . . . . . "https://www.ukrlp.co.uk"^^ . "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1"^^ . . . . . . . . "P683" . "false"^^ . "http://cgsc.biology.yale.edu/index.php"^^ . . "Internet Engineering Task Force Language Tag" . . "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . "ontology" . . "false"^^ . . . "Clytia hemisphaerica Development and Anatomy Ontology" . . . . . . . . "TP53"^^ . . . . . "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . "Yeast Phenotype Ontology" . . "interaction" . "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . . . "Vocabulary of Interlinked Datasets" . "Browser for the periodic table of the elements"^^ . . "obo" . . . . . . "Ontology for General Medical Science" . . . . "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^ . . . "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1"^^ . . "http://www.antirrhinum.net/"^^ . "https://cropontology.org/ontology/CO_322/Maize"^^ . "https://bioportal.bioontology.org/ontologies/EDDA"^^ . "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . "comparative genomics" . . . "ontology" . . . . "development" . . "human" . . . . "http://europepmc.org/"^^ . . . . "obo" . "https://www.rhea-db.org/rhea/$1"^^ . "https://www.expasy.org/prosite/"^^ . . "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources."^^ . "Hathi Trust Digital Library" . "frederic.bastian@unil.ch" . "0000062"^^ . . . . . . . . . . . . . "WikiPathways is a database of biological pathways maintained by and for the scientific community."^^ . "life science" . "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters"^^ . . . . . "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . . . "false"^^ . . . "https://www.fdilab.org"^^ . . . . . "ontology" . . . "obo" . "https://www.ncbi.nlm.nih.gov/protein"^^ . . . . . "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . . "Mark Engelstad" . "false"^^ . . . "http://www.ebi.ac.uk/astd/geneview.html?acc=$1"^^ . "false"^^ . . . "^DB\\d{5}$"^^ . "http://yetfasco.ccbr.utoronto.ca/"^^ . "plant breeding" . . "AHR"^^ . . . . . "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . "http://www.jcvi.org/mpidb/about.php"^^ . . "A type for entries in the Bioregistry's registry." . . . . "0000010"^^ . . . . "^\\d+$"^^ . "^\\d+$"^^ . . . . "Database of RNA Junctions and Kissing loop Structures" . "https://aopwiki.org/"^^ . "virology" . . . . . "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . . . "false"^^ . . . . . "Bob Thacker" . . . . "http://www.cellsignal.com/catalog/index.html"^^ . "https://github.com/carrineblank/MicrO"^^ . . . "obo" . . . . . "false"^^ . "subject agnostic" . . "https://github.com/phenoscape/teleost-taxonomy-ontology"^^ . _:Nde8f4edac5f842de94322e9a72f74049 "ncictcaehelp@mail.nih.gov" . "0010039"^^ . . . . "false"^^ . . "^CHEMBL\\d+$"^^ . "false"^^ . . "FlyBase Gene" . . "https://data.bloodpac.org/."^^ . . . "ontology" . "^\\d\\w+$"^^ . "^ENSG\\d{11}$"^^ . "^\\d+$"^^ . . . . . . "^\\w+$"^^ . "Wormbase Gene ID" . "^\\w+$"^^ . "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . . . "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^ . "BIOMD0000000048"^^ . . . . "NLXBR" . . "Alex Bateman" . . . . . . "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . "https://github.com/OOSTT/OOSTT"^^ . . . . "SNOMEDCT_US_2018_09_01" . . . . . "Protein modification" . . "false"^^ . "https://www.datascienceontology.org/"^^ . . . . "gene expression" . "false"^^ . . "life science" . "life science" . "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . . "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . . "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . . . "rna" . . . "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . . . . . "taxonomy" . . . . "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^ . . . . . "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . "Human developmental anatomy, abstract" . . . . "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^ . . . "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1"^^ . . . . . . "RID1"^^ . "protein" . "chemistry" . . . "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . "rxn00001"^^ . "biochemistry" . "https://biopragmatics.github.io/providers/dhba/$1"^^ . . . . . . . . . . "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards."^^ . "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . . . "Bgee gene" . . "sheriff@ebi.ac.uk" . . . . "false"^^ . "https://glycopost.glycosmos.org/entry/$1"^^ . . . "33607"^^ . "https://fungidb.org/fungidb/app/record/gene/$1"^^ . "false"^^ . . . . . "false"^^ . . . . . . . . "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . . "http://www.ensembl.org/"^^ . "http://www.depod.bioss.uni-freiburg.de"^^ . "^[a-z0-9\\_]+$"^^ . "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."^^ . "https://licebase.org"^^ . "HL7 V2 Code Systems" . . "https://civicdb.org/"^^ . . . . . . . . "false"^^ . "http://bioinfo.lifl.fr/norine/"^^ . "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . . . . "http://www.ontologyrepository.com"^^ . "false"^^ . . . "health science" . . "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . "^[0-9]{10}$"^^ . "structure" . "Andreas Ledl" . . . "veNOG12876"^^ . "Chemical Entities of Biological Interest" . . . . . . . . . . . "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . . . . . "false"^^ . . . . "http://www.kazusa.or.jp/codon/"^^ . . . . . "HD+118-001"^^ . . . "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . "false"^^ . "https://www.gtexportal.org/home/gene/$1"^^ . . . . . "1868"^^ . "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . "http://bioinformatics.ramapo.edu/GRSDB2/"^^ . . . . . . "http://purl.obolibrary.org/obo/RNAO_$1"^^ . . "Probes and Drugs" . . "0000001"^^ . . . . . . "http://genex.hgu.mrc.ac.uk/"^^ . . . . "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . . . "https://pharmacome.github.io/conso/$1"^^ . . . . . "medicine" . . "false"^^ . . . . "SNOMEDCT_US" . . . . . "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . . . . . "gene expression" . . . . . . "lagonzalezmo@unal.edu.co" . . "http://purl.obolibrary.org/obo/CTO_$1"^^ . "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . . . . . . "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains."^^ . . "Q9UKQ2"^^ . "http://proteomecentral.proteomexchange.org/"^^ . "protein" . . . . . . . . . "^\\d{4}$"^^ . "PMC3084216"^^ . . . . . . "^IS\\w+(\\-\\d)?$"^^ . "ontology" . . "subject agnostic" . . . "bioinformatics" . . "small molecule" . "ontology" . "^[0-9]+$"^^ . "A database containing predicted viral miRNA candidate hairpins."^^ . . "^NPC\\d+$"^^ . . "false"^^ . . . . "Simple Knowledge Organization System eXtension for Labels" . . "Transcription Factor Database" . . . "00073"^^ . "^RCB\\d+$"^^ . . . . . "5.1"^^ . "proteomics" . . . "ask-epd@googlegroups.com" . "false"^^ . "http://purl.org/dc/dcmitype/$1"^^ . . . "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1"^^ . . . . . . . . "false"^^ . "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . "meetings" . "0000038"^^ . . . "^\\d{7}$"^^ . . . "C34"^^ . . . "ontology" . . . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues."^^ . . "^IHW\\d+$"^^ . . "agriculture" . . . . "NMR Restraints Grid" . . . "UMLS_ICD9CM_2005_AUI" . . . . . . . . "proteomics" . . . "ontology" . "pier.buttigieg@awi.de" . "life science" . . . . . "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . "life science" . . . . . "genome" . "0000000"^^ . _:N493d7c9d64514017b982cfcb06ea2146 "Cynthia Hake" . . "http://ecolexicon.ugr.es/en/index.htm"^^ . "NCBI_Taxon_ID" . . . . "^\\d+$"^^ . . . . "pgxbs-kftva5zv"^^ . . "false"^^ . . . "https://github.com/phenoscape/vertebrate-taxonomy-ontology"^^ . "goccid" . . "Blue Brain Project Knowledge Graph" . . _:N75256e4abe3741d89b282c13292812f5 . "^\\d{7}$"^^ . "false"^^ . . . . "genome" . . . "genomics" . . "familyName"^^ . . . "false"^^ . "phylogeny" . . . . "0000139"^^ . . . "http://purl.obolibrary.org/obo/MMUSDV_$1"^^ . . . . "http://www.proteomexchange.org/"^^ . "false"^^ . . . . . . . . . . "genome" . . . . "^\\d+$"^^ . . "KEGG.COMPOUND" . . . . . . "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . . . . . . . "Brachiaria ontology" . "^\\d{7}$"^^ . . . "ontology" . . . "1"^^ . "Cell line databases/resources"^^ . . "false"^^ . . "false"^^ . . . "gianni.cesareni@torvergata.it" . . . . "false"^^ . . "http://urgi.versailles.inra.fr/Genefarm/"^^ . "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . . "kegg_genome" . . "1.1.1.1"^^ . . . _:N43f2c74a5fec40a29249bab92c0ad2b5 "Allen Institute for Brain Science" . . . . . . . . . . "botany" . . . . . . . . . "false"^^ . . _:Nfd007d2ce9024cafa9b0c7bc966de6cc . . . "ontology" . . . . "https://www.google.com/patents/$1"^^ . . "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . "BCRTi001-A"^^ . "http://lsdis.cs.uga.edu/projects/glycomics/propreo/"^^ . "^\\d{7}$"^^ . "GitHub Issue" . "https://biopragmatics.github.io/providers/pba/$1"^^ . . "https://depmap.org/portal/cell_line/$1"^^ . "false"^^ . "PharmGKB" . . . . . "http://hymao.org"^^ . . "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . "false"^^ . "biomedical science" . "biomedical science" . . "structure" . . "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex)."^^ . "ontology" . "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1"^^ . . . "^\\d{7}$"^^ . "obo" . . "life science" . . . . . . . "genome" . . "ontology" . "pathobiochemistry" . "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1"^^ . "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013."^^ . "EC number" . . . . "false"^^ . . . . . "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"^^ . "090803"^^ . . "xeni.kechagioglou@lifewatch.eu" . . "cell biology" . "ontology" . "http://purl.obolibrary.org/obo/PAO_$1"^^ . . . . "Ontology about the development and life stages of the C. elegans"^^ . . "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . . "^SEQF\\d+$"^^ . . "https://github.com/BgeeDB/confidence-information-ontology"^^ . "https://www.yeastgenome.org/locus/$1"^^ . "https://www.arraymap.org/pgx:$1"^^ . . "http://hpc-bioinformatics.cineca.it/fusion/main"^^ . . . . "false"^^ . . "ProtClustDB" . . "https://vocab.lternet.edu/vocab/vocab/index.php"^^ . "taxonomy" . . . . . . . . "Orphanet" . . "Rv1908c"^^ . . "stacia@stanford.edu" . "Identifier for a species in iNaturalist"^^ . "genomics" . . . "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . . . . . . . . . "https://civicdb.org/links/drugs/$1"^^ . "^K[0-9]+$"^^ . . . . . "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . "false"^^ . . . . "https://www.ebi.ac.uk/chebi/"^^ . . "protein" . . . . "dna" . . . . . "pharmacogenomics" . "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . "26957"^^ . . . . "0000423"^^ . "biocuration" . "agronomy" . . "gobpid" . . . . . "MEROPS Entry" . "Vocabulary used in the RDF representation of SBML models."^^ . . . . . . "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . "computational biology" . "Database of Quantitative Cellular Signaling: Pathway" . . . "The Bioregistry's meta-registry"^^ . "genetics" . . . "KEGG-path" . "RNA SSTRAND" . "0002502"^^ . "true"^^ . . "ontology" . . . . "farming systems research" . "botany" . . "metascience" . "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . "http://www.unimod.org/"^^ . "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models"^^ . "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . . "false"^^ . . "botany" . . . "interaction" . . . "^[a-zA-Z0-9-]+$"^^ . "protein" . . . . "false"^^ . . . . . "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php"^^ . "https://www.ebi.ac.uk/pdbe/emdb/"^^ . . "^\\d+$"^^ . "http://purl.obolibrary.org/obo/MFMO_$1"^^ . . "^CAL\\d{7}$"^^ . . "phenomics" . . . . . "2A"^^ . "false"^^ . . "biomedical science" . "environmental science" . . . . . . "http://purl.enanomapper.org/onto/ENM_$1"^^ . . "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . . "http://www.informatics.jax.org/expression.shtml"^^ . "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance."^^ . . . . . "sequence" . . . . . . . "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^ . . . . . . . . . "^\\d+$"^^ . "0000072"^^ . "AOPWiki (Key Event Relationship)" . . . . . . . . . . . "Maize gross anatomy"^^ . . . . . . . "false"^^ . . "LIPID MAPS" . . "http://bactibase.hammamilab.org"^^ . "genome" . . . . "http://senselab.med.yale.edu/OdorDB"^^ . . "protein" . "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . "dictyBase" . . "https://cellmodelpassports.sanger.ac.uk/"^^ . . . "5HT3Arano"^^ . . . "life science" . . . "Bioregistry" . "nstd102"^^ . "false"^^ . . "ontology" . . _:N7b0adfbcb6ec489288af6f3da845e1f1 . . . . . . . "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . "151022"^^ . . . . . "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^ . . . . "obo" . . "false"^^ . . . . "genome" . "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^ . . "https://fungi.ensembl.org/id/$1"^^ . "https://www.yeastgenome.org/observable/APO:$1"^^ . "proteomics" . . "nucleotide" . . "https://www.ncbi.nlm.nih.gov/dbvar"^^ . . "Homeodomain Research" . . . . _:Na7345ed3b17d42ffa48b62644523a903 "helpdesk@cropontology-curationtool.org" . . . "life science" . . . . . . . "true"^^ . . . . . "Mass spectrometry ontology" . . "false"^^ . . . . . . . . . . . "Endogenous Regulatory OligoPeptide knowledgebase-Moscow" . . . . . . . . "ontology" . . "^\\d{7}$"^^ . . "Gender, Sex, and Sexual Orientation Ontology" . . "bioinformatics" . "Molecular Interactions Controlled Vocabulary" . "neuroscience" . "^[A-Za-z0-9\\-\\/]+$"^^ . . . . "ontology" . . . . "protein" . "^\\d+$"^^ . . . "https://foodb.ca/foods/$1"^^ . "phylogeny" . . . "obo" . . . "kdurante@stanford.edu" . "false"^^ . . . . . "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . . . . . . . . "http://www.w3.org/2002/07/owl#$1"^^ . "A manually curated resource for the representation and annotation of metabolic pathways"^^ . "cjmungall@lbl.gov" . . "265912"^^ . . "true"^^ . . "metabolomics" . "natural science" . . "false"^^ . . "false"^^ . "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^ . "g.gkoutos@bham.ac.uk" . . "false"^^ . . . "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once."^^ . . "3447"^^ . "21723"^^ . "http://purl.obolibrary.org/obo/AISM_$1"^^ . . "false"^^ . "dna" . . . . "false"^^ . "^\\d+$"^^ . "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . . . . . . "^\\d+$"^^ . . "^\\d+$"^^ . . "Scientific Evidence and Provenance Information Ontology" . . . . . . "^(\\d+)|(\\w+)$"^^ . "true"^^ . . . . . . "A hierarchical classification of congenital heart disease "^^ . "ICD-11" . . . . . . . . . . "Castor bean ontology" . . "false"^^ . . . . "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . . "jrsmith@mcw.edu" . "Sweet Potato ontology" . "business administration" . "dna" . . . "http://purl.obolibrary.org/obo/OMP_$1"^^ . . . . "Human Gene Mutation Database" . . . . . . . "false"^^ . . . . "http://www.bmrb.wisc.edu/"^^ . . . . "UBERON" . . . . . "https://mint.bio.uniroma2.it"^^ . . . "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . . "https://github.com/SciCrunch/NIF-Ontology"^^ . "NIF Standard Ontology: Organisms" . . . . . "https://nanocommons.github.io/identifiers/registry#$1"^^ . "http://sweetontology.net/matrMineral/$1"^^ . "Human Phenotype Ontology" . . . "000140" . . . . . . . . . . . . . . . . . . . "msig" . . . "William Hogan" . . "Scholia Registry" . "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.)."^^ . . . . . . "Subcellular Anatomy Ontology" . . "http://ardb.cbcb.umd.edu/"^^ . . . . _:Nab1953a6cd9f4ba6962b9ebdf698221d "Heinrich Herre" . . . "^(ENSFM|ENSGTV:)\\d+$"^^ . . . . . "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . . . "https://human.brain-map.org"^^ . . "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . "ontology" . . "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . . . . "https://publons.com/researcher/$1"^^ . "ECU03_0820i"^^ . . . . . . "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . "Oryzabase Stage" . "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . "slm" . "https://github.com/obophenotype/c-elegans-phenotype-ontology"^^ . . "https://www.metanetx.org/chem_info/$1"^^ . . . . . . "chenyangnutrition@gmail.com" . . "molecular biology" . . . . . "^(\\w){3}$"^^ . "^.*?--%3E.*?$"^^ . "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki"^^ . . "http://matrixdb.univ-lyon1.fr/"^^ . . . . . . . "obo" . . . "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . . . . . . . "https://www.phenxtoolkit.org/"^^ . "63"^^ . . "policy" . . . . . . . . "classification" . . "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"^^ . . . . . . . "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . "http://prodom.prabi.fr/prodom/current/html/home.php"^^ . . . "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . . . . . . . . . "false"^^ . . "^ECMDB\\d+$"^^ . . "Fungal gross anatomy" . . . . . . . . . . "false"^^ . . . . "pathway" . . . "http://purl.obolibrary.org/obo/HSO_$1"^^ . "jgraybeal@stanford.edu" . . . "^[A-Z\\-]+$"^^ . . . . . "NIF Standard Ontology: Qualities" . "false"^^ . "obo" . "ontology" . . . . "torsten.schwede@unibas.ch" . . "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist"^^ . "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure."^^ . "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . . . . . "N1899"^^ . . "false"^^ . "genome" . . . . . . . "protein" . . "^M\\d{4}$"^^ . "Observational Medical Outcomes Partnership" . . . . . "ontology" . . . . . . . . "obo" . . . "http://multicellds.org/MultiCellDB.php"^^ . "^RF\\d{5}$"^^ . "^CHEMBL\\d+$"^^ . _:N7849db7d34ce4ffcb9aa008600a73c2f "whocc@fhi.no" . . "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^ . "240-17-488-3-4-12"^^ . "CAID" . . "http://www.pharmgkb.org/"^^ . "50943"^^ . . . "Anatomical Entity Ontology" . "false"^^ . "Uberon" . . . "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc."^^ . . . . "https://bioregistry.io/resolve/github/pull/$1"^^ . . . . . . . "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . . "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . . "FundRef" . . "agriculture" . "^[0-9A-Za-z\\-.]+$"^^ . . . . . . . "Association-Rule-Based Annotator" . "LINCS Small Molecule" . . . . "ontology" . . . . "56586"^^ . "botany" . . . . . "Virtual Fly Brain" . "biomedical science" . . "Kim Durante" . . . . . "drug metabolism" . . . "life science" . . "ChEMBL-Cells" . "http://pax-db.org/"^^ . "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait"^^ . . "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^ . . . . . . "rs11603840"^^ . . "true"^^ . "https://www.merckmillipore.com/"^^ . . . . "Lars Holm Nielsen" . . . "false"^^ . . . "dc11" . . _:Nef79f01544844c5d8c213672c7550747 "Usha Mahadevan" . . . . "^\\w+$"^^ . . . "^\\d{7}$"^^ . "https://cropontology.org/rdf/CO_322:$1"^^ . "false"^^ . . . . "mathematics" . "^[0-9]+$"^^ . "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue."^^ . "European Bank for induced pluripotent Stem Cells" . "^\\d{8}$"^^ . "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1"^^ . "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^ . . "https://www.re3data.org" . . "http://exac.broadinstitute.org/"^^ . . "https://labsyspharm.github.io/lspci/$1"^^ . "https://www.checklistbank.org/dataset/$1"^^ . . . . "https://biopragmatics.github.io/providers/goche/$1"^^ . . . "^\\d+$"^^ . . . _:N9b124bbcf45f46b89f01336eacbea6ed "fred@fgiasson.com" . . . "obo" . "biochemistry" . "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"^^ . . . "cell lines" . . . . "true"^^ . . . . . _:N6e73b3356d344c19bd4b22fe2f81c6fd . "nucleotide" . "NASC code" . . . "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . . . "false"^^ . . . "Martin Kuiper" . . . . "Golm Metabolome Database GC-MS spectra" . . . . . . "https://www.ebi.ac.uk/miriam/"^^ . "genome" . . . "http://vita.mbc.nctu.edu.tw/"^^ . . "Robert Court" . "BioGRID" . "Getty Thesaurus of Geographic Names" . . . "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . "genome" . _:Nc0a8f25e59214179839d6cce00bbed5d "Pierre Sprumont" . . . . . "^LSM-\\d+$"^^ . "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates."^^ . "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E."^^ . "false"^^ . "Val Wood" . . . . . "RNACentral ID" . . . . . "life science" . "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . "true"^^ . "^[0-9]+-[0-9]+$"^^ . "Paul Fabry" . . . "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"^^ . . "virology" . "Pathguide" . . . "C2584994"^^ . "https://glytoucan.org/"^^ . "https://sed-ml.org/urns.html#language:$1"^^ . "false"^^ . "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . "true"^^ . . "^PGS[0-9]{6}$"^^ . "Q-2958"^^ . . . . . . . . . . . . "https://ligandbook.org/package/$1"^^ . "Oryzabase Reference" . "http://www.kupkb.org/"^^ . . . . . . "genomics" . "https://swbiodiversity.org/seinet/index.php"^^ . . . . "General Standard for Food Additives Online Database" . . "1kfv"^^ . . "earth science" . "gene expression" . . . . . . "H-InvDb Transcript" . . . . . "GR_QTL" . . "life science" . "TIGR protein families" . "ontology" . . "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . . "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . . . "Drosophila Genomics Resource Center" . . "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . . . . . . . "life science" . . . . "https://reporter.nih.gov/"^^ . . . . . . . . "dictyBase" . . . . . . . . . . . "https://pubchem.ncbi.nlm.nih.gov/periodic-table"^^ . "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt"^^ . . . . "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . . . "TA14985"^^ . . . . . "75"^^ . . . . . "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . . . . "CLV_MEL_PAP_1"^^ . . . . . . . . . . . "0000006"^^ . . "Literature references in Gramene"^^ . . "https://reactome.org/content/detail/$1"^^ . . . . . . . . . "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . . . . . . . . "RNA Virus Database" . . "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . . "protein" . . . . . . "small molecule" . "https://purl.dataone.org/odo/MOSAIC_$1"^^ . "http://mged.sourceforge.net/ontologies/MGEDontology.php"^^ . "false"^^ . . "false"^^ . "data management" . . . "false"^^ . . . . . . . . . "virus" . . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . "^[a-z]+(\\..*?)?$"^^ . . "chemical" . "allergen" . . . "http://multicellds.org/MultiCellDB/$1"^^ . . . . . "false"^^ . "obo" . . . . "ribocenter" . . . . . "Li7"^^ . . . "obo" . . "Gene Ontology Registry" . "genomics" . . "207LH0002X"^^ . . "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information."^^ . . _:N0893f99407384693ba14665e70f20955 "wbug@ncmir.ucsd.edu" . "762"^^ . . . "ACH-000001"^^ . "TTHERM_00648910"^^ . . . "Small Molecule Pathway Database" . "Life cycle stages for Medaka"^^ . . . . "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^ . . "ApiDB_PlasmoDB" . "NCBITaxon" . "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . . "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . . "false"^^ . . "http://bioinfo.mbb.yale.edu/MolMovDB/"^^ . . . . . . "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . . . "MmusDv" . . "LSM-6306"^^ . . . "^PA\\w+$"^^ . "false"^^ . "pierre.grenon@ifomis.uni-saarland.de" . . . "epigenetics" . . "000004"^^ . . "Collection" . . "http://world-2dpage.expasy.org/repository/"^^ . "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins."^^ . . . "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . "Petra Fey" . "TubercuList" . . . . . . . "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1"^^ . . . "false"^^ . . . . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . "false"^^ . . . . . "D00123"^^ . "jaiswalp@science.oregonstate.edu" . "psychology" . . . . . "protein" . . . "^\\d{7}$"^^ . . . "https://fairsharing.org/$1"^^ . . . "ontology" . . . . . . "^[A-Z0-9]{6,7}$"^^ . "PSI-MI" . . . "https://linkml.io/linkml-model/docs/SchemaDefinition/"^^ . "ontology and terminology" . . . _:N23e1872969314fefb130ea79e8c9dfa8 . . "^ACYPI\\d{6}(-RA)?$"^^ . . "54"^^ . . "Silvio Peroni" . . "false"^^ . . . . . . . "false"^^ . "Event (INOH pathway ontology)" . "functional genomics" . . . . "2404"^^ . "https://ssbd.riken.jp/database/project/$1"^^ . "^\\d+$"^^ . . "support@bioontology.org" . . . "gene" . . "53784"^^ . . "https://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=UBERON:$1"^^ . "^\\d{7}$"^^ . "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . . "Wasila Dahdul" . "https://portal.bluebrain.epfl.ch"^^ . . "protein" . . "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects."^^ . "IPD-IMGT/HLA" . . . "Rfam database of RNA families" . . . "http://doqcs.ncbs.res.in/"^^ . "false"^^ . . . "Ontology about the gross anatomy of the C. elegans"^^ . . "Google Patents" . "false"^^ . "UniProt Isoform" . "^\\d+$"^^ . . . . . . . . "^\\d{7}$"^^ . . "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions."^^ . . "botany" . . . "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . . . _:N567f33f5295044b58ac093dc68207b3f "custserv@nlm.nih.gov" . _:Ncd1f565b02cb46078547f9a2ec5e79b6 "Allotrope Foundation" . . "life science" . . "life science" . . . . "UPPRO" . "0002005"^^ . "http://www.cazy.org/"^^ . "OSR0818"^^ . . "FB" . . . . . . . "false"^^ . "mirTarBase ID" . "false"^^ . . . . "4DN" . . . . "^\\d+$"^^ . . "selventa" . "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . . "http://classyfire.wishartlab.com/"^^ . . . . . . . . "^\\d+$"^^ . . . . . . . . "biomedical science" . . . "enzyme" . . "Informed Consent Ontology" . . . "https://www.cdc.gov/nchs/icd/icd9.htm"^^ . . . "true"^^ . . . . . . "Open Researcher and Contributor" . . . "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release)."^^ . . "vendor" . . . "0000046"^^ . "genome" . . . "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . "https://pubchem.ncbi.nlm.nih.gov/source/hsdb"^^ . "true"^^ . . . "systems biology" . . . "https://metabolicatlas.org"^^ . "^[A-Za-z0-9]+$"^^ . . . . "false"^^ . . . . "Mouse adult gross anatomy" . . "biomedical science" . . "biology" . "false"^^ . "Bibliometric Data Ontology" . "AGRO" . "Models developed with the Virtual Cell (VCell) software prorgam."^^ . . . . "^\\d{7}$"^^ . . "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . . "^\\d{7}$"^^ . "0000086"^^ . "http://lincsportal.ccs.miami.edu/SmallMolecules/"^^ . . . . . "false"^^ . "^\\d+$"^^ . "Pierre-Marie Allard" . "https://www.ebi.ac.uk/ols/ontologies/$1" . . . . "false"^^ . "natural history" . . . . . . "http://genomics.senescence.info/genes/"^^ . . . "neurology" . . . . . "David Blackburn" . "http://merops.sanger.ac.uk/index.htm"^^ . "true"^^ . . "ontology" . . . . . . . . . "taxonomy" . . "rna" . "Pierre-Alain Binz" . . . "8639.1"^^ . . . . . "ontology" . "BioPortal" . "Drug_Central" . . . . . "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . . "^FOOD\\d+$"^^ . "biology" . . . "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . "GLAndersen@lbl.gov" . . . . . . . . . . . "protein" . "^(\\w+)?\\d+$"^^ . . . "^\\w+:[\\w\\d\\.-]*$"^^ . . "Candida Genome Database" . "^\\w+$"^^ . . . . . . "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^ . . . . "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . . . "reaction" . . "life science" . "^\\d{7}$"^^ . . "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . "false"^^ . . "developmental biology" . . . . . "false"^^ . "^DP\\d{5}r\\d{3}$"^^ . . "https://www.gwascentral.org/phenotypes"^^ . . . . . "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . . . "NOAA Fisheries Species Directory" . . "BioMagResBank" . "^\\d{7}$"^^ . "ontology" . "protein" . . "ontology" . . "ontology" . "3G6A5W338E"^^ . . "ontology" . "12dgr161"^^ . "AADB12"^^ . "false"^^ . . . . . . . . _:Ndd2597b2adc04c7b85ebc82d11dfc398 "Fahim Imam" . . "false"^^ . "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . . "http://www.kegg.jp/entry/$1"^^ . "genome" . "true"^^ . . "genomics" . . "YRC PDR" . . . "http://purl.obolibrary.org/obo/PCO_$1"^^ . "virology" . . . "https://github.com/PlantPhenoOntology/PPO"^^ . "ontology" . _:N9cb3481def5944cba2054f5a94be0c79 "Ian Davis" . . "^\\d{8}$"^^ . "false"^^ . . . "ontology" . . "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . "FunderRegistry" . "gene" . . . . "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^ . . . . "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"^^ . "RGD Disease Ontology" . . . . . "101"^^ . . . . . . . "http://purl.obolibrary.org/obo/COVIDO_$1"^^ . . . . . "false"^^ . . . . . "^\\d+$"^^ . . . "http://data.europa.eu/89h/$1"^^ . . . . . "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . "An experimental run, served thrugh the ENA"^^ . "/53355/cl010066723"^^ . "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^ . . . "obo" . "human" . . . "http://purl.obolibrary.org/obo/TRANS_$1"^^ . . . . "http://www.mesquiteproject.org/ontology/Habronattus/index.html"^^ . "AAC"^^ . . . . "^\\d+$"^^ . "false"^^ . . . . "false"^^ . . . . . . . . . "Mosquito gross anatomy ontology" . . . . . . . "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"^^ . . . . . . . "aquaculture" . "false"^^ . . . . "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . . "cthoyt@gmail.com" . . "http://rulai.cshl.edu/TRED"^^ . . "^UPI[A-F0-9]{10}$"^^ . . . "PubChem Element" . . "false"^^ . . . . "http://prism.case.edu/prism/index.php/EpilepsyOntology"^^ . . . . . . . "The Ontology of Genes and Genomes" . . . "obo" . . . . "true"^^ . "Yeast Intron Database v4.3" . . . . . "protein" . . . "10.1621/vwN2g2HaX3"^^ . "SNOMEDCT_2010_1_31" . "false"^^ . . . "eukaryotic" . . "EC number" . . . . . . . "E-cyanobacterium entity" . "https://www.ncbi.nlm.nih.gov/medgen/"^^ . "eVOC mouse development stage" . . . "Software"^^ . . . "chemical" . . . . . . "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . "mammalian" . "obo" . "http://ifomis.org/bfo/"^^ . . . . "811"^^ . "BindingDB" . "LipidBank" . "life science" . "P00266"^^ . "false"^^ . "false"^^ . . "https://www.w3.org/TR/shacl/"^^ . . . "http://www.alanwood.net/pesticides/$1.html"^^ . . . "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc."^^ . . "UR000124451"^^ . "^\\d+$"^^ . . . . . . "http://msi-ontology.sourceforge.net/"^^ . "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . "FlyBase Controlled Vocabulary" . "UM-BBD_pathwayID" . "Accession number of an entry from the BIND database."^^ . . . . . "Mammalia Polymorphism Database" . . "Unified Medical Language System Atomic Unique Identifier" . "genomics" . "biomedical science" . "false"^^ . "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"^^ . "https://lotus.naturalproducts.net"^^ . "biomedical science" . . . "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . . . "https://github.com/rsc-ontologies/rsc-cmo"^^ . "proteomics" . . . . . . "SMID-DB" . "https://cameo3d.org"^^ . "Signaling Network Open Resource" . . "comparative genomics" . . "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . . "https://restraintsgrid.bmrb.io/NRG/MRGridServlet"^^ . . . "genome" . . . . . "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . . . . "biosimulations" . . . "http://n2t.net/ark:$1"^^ . . . "pubchem_id" . "^[0-9\\.]+$"^^ . . "1426686"^^ . . . "Probability Distribution Ontology" . . . . "biomedical science" . "http://www.nlm.nih.gov/medlineplus/"^^ . . "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1"^^ . . "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . . "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe."^^ . . . . . "false"^^ . . . "https://github.com/pombase/fypo"^^ . "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . "false"^^ . "ChemIDplus" . . "https://github.com/DiseaseOntology/PathogenTransmissionOntology"^^ . . "ontology" . "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . . "http://wheat.pw.usda.gov"^^ . . . "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . . "https://cropontology.org/ontology/CO_346/Mungbean"^^ . . "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^ . . . "false"^^ . "http://smart.embl-heidelberg.de/"^^ . . . "^\\d+$"^^ . . . . "false"^^ . . "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant."^^ . . . . "SBML RDF Vocabulary" . . . . . "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^ . . "Jianmin Wu" . . "biodiversity" . "anatomy" . . . . . . . . "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . . . . . . . "life science" . . . . . . . "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^ . . . . . . . . . . "Flora Phenotype Ontology" . . . "anatomy" . . "SNOMED CT (International Edition)" . "agriculture" . . . . . . "https://www.sigmaaldrich.com"^^ . "false"^^ . "https://loinc.org/$1"^^ . . "biology" . . "http://greengenes.lbl.gov/"^^ . "http://www.geneontology.org/gocam"^^ . "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"^^ . "rna" . "https://mips.helmholtz-muenchen.de/genre/proj/corum/"^^ . . . . "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . "disease" . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . "obo" . . . "life science" . . "MNXR101574"^^ . . . . . . "^\\d{7}$"^^ . . . . . _:N2ed1e738ada64dc8b13c1627aa247491 "Laia Subirats" . . . "false"^^ . . . "300165/p13898_2106T"^^ . . . . . . . . . "oct 2016"^^ . "comparative genomics" . "Bactibase" . "functional genomics" . . . . . . . . "false"^^ . "https://pbil.univ-lyon1.fr/databases/hovergen.php"^^ . "67"^^ . . . . "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^ . . "protein" . "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . . "biomedical science" . "Gmelins Handbuch der anorganischen Chemie" . . . "rna" . "false"^^ . "false"^^ . . . . . . "omics" . . "false"^^ . . . . "true"^^ . . "GALEN" . . . . "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . . . "^[A-Z]+[0-9]+$"^^ . . . . "AKR-270"^^ . . "epigenetics" . . . . . . . . "http://www.cabri.org/"^^ . "Sabine.Oesterle@sib.swiss" . . "https://github.com/semanticchemistry/semanticchemistry"^^ . "^\\d+$"^^ . "https://github.com/information-artifact-ontology/ontology-metadata"^^ . . "life science" . . "ontology and terminology" . . "ontology" . "http://www.ebi.ac.uk/cmpo"^^ . "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . . "false"^^ . . . "dna" . . "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . "http://caps.ncbs.res.in/SSTOSS/index.htm"^^ . . "http://datf.cbi.pku.edu.cn/"^^ . "sequence" . . . "https://glycopost.glycosmos.org"^^ . . "Cowpea ontology" . . "https://vcell.org/biomodel-$1"^^ . "http://www.cathdb.info/"^^ . _:N77e79fb933594bbf9c63bd2ee92c2e2a "curator@inoh.org" . "false"^^ . . "false"^^ . . . . . . "small molecules" . . . "NINDS Human Cell and Data Repository" . _:N6216cc9360e94e9abe37b18746f3c0d6 "henrich@embl.de" . . . . . "transcriptomics" . "https://www.pgscatalog.org/pgs/$1"^^ . "social science" . . "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . . . . "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . . . "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . . . _:N39abf46a000a41bf90661a794ec6ea74 "Sergio José Rodríguez Méndez" . "classification" . . "STUDY1040"^^ . . . . . . . "false"^^ . . . . . . "dna" . "protein" . . . "genome" . "http://www.gramene.org/"^^ . . "^\\d{7}$"^^ . "ADA"^^ . . . . . "bioinformatics" . . "data mining" . . "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . . . "false"^^ . . . . . "^\\d+$"^^ . "c.dudek@tu-braunschweig.de" . . . . . "^\\d{7}$"^^ . . . "false"^^ . "Experimental condition ontology" . . . . . . "E-MEXP-1712"^^ . . . "genome" . "protein" . "Web Ontology Language" . . "https://registry.identifiers.org/registry?query=MIR:$1"^^ . "EDAM Data" . . "false"^^ . . . . . . "false"^^ . "^\\d{7}$"^^ . . . . . "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^ . . "https://w3id.org/hso"^^ . "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . . "Defunct vaccine information source from the He Lab"^^ . . . . . . . "https://www.rebuildingakidney.org/"^^ . . "^SAM[NED](\\w)?\\d+$"^^ . . "Proteoform Atlas" . "false"^^ . . "https://icd.codes/icd10cm/$1"^^ . . "dna" . . . . . . . . "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . . . "UniProt Proteomes" . . . . . . "http://www.pdb.org/"^^ . "http://redfly.ccr.buffalo.edu"^^ . . . . "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . "ThermoFisher is a life sciences supply vendor."^^ . . "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . . "http://stitch.embl.de/"^^ . . "genetics" . "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th leve