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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
DATFAP
 
Resource Report
Resource Website
DATFAP (RRID:SCR_005413) DATFAP data or information resource, database A database of transcription factors from 13 plant species, and PCR primers for around 90% of them. homolog, sequence, transcription factor is listed by: OMICtools
is related to: Gene Ontology
PMID:18366738 Free OMICS_00552 SCR_005413 Database of transcription factors with alignments and primers 2026-08-03 09:32:40 0
FuncExpression
 
Resource Report
Resource Website
FuncExpression (RRID:SCR_005773) FuncExpression data analysis service, service resource, analysis service resource, production service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 11, 2012. FuncExpression is a web-based resource for functional interpretation of large scale genomics data. FuncExpression can be used for the functional comparison of plant, animal, and fungal gene name lists generated from genomics and proteomics experiments. Multiple gene lists can be classified, compared and visualized. FuncExpression supports two way-integration of plant gene functional information and the gene expression data, which allows for further cross-validation with plant microarray data from related experiments at BarleyBase. Platform: Online tool statistical analysis, genomics, compare, function, plant, animal, fungus, gene, proteomics, gene expression, microarray is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: PLEXdb - Plant Expression Database
has parent organization: Iowa State University; Iowa; USA
THIS RESOURCE IS NO LONGER IN SERVICE nlx_149237 SCR_005773 2026-08-03 09:32:56 0
ProfCom - Profiling of complex functionality
 
Resource Report
Resource Website
1+ mentions
ProfCom - Profiling of complex functionality (RRID:SCR_005797) ProfCom data analysis service, service resource, analysis service resource, production service resource Profiling of Complex Functionality (ProfCom) is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of complex function. A complex function is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. Platform: Online tool gene, function, profile, gene ontology, complex function, statistical analysis, bio.tools is listed by: Gene Ontology Tools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
has parent organization: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany
DFG PMID:16959266 Free for academic use biotools:profcom, nlx_149276 https://bio.tools/profcom SCR_005797 Profiling of Complex Functionality, Profiling of Complex Functionality (ProfCom) 2026-08-03 09:32:56 4
SerbGO
 
Resource Report
Resource Website
SerbGO (RRID:SCR_005798) SerbGO data analysis service, service resource, analysis service resource, production service resource SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one. Platform: Online tool microarray, gene expression, statistical analysis, gene ontology, bio.tools is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: University of Barcelona; Barcelona; Spain
PMID:18480123 Free for academic use nlx_149286, biotools:serbgo https://bio.tools/serbgo SCR_005798 SerbGO - Searching the best GO Tool 2026-08-03 09:32:56 0
GOtcha
 
Resource Report
Resource Website
1+ mentions
GOtcha (RRID:SCR_005790) GOtcha data analysis service, service resource, analysis service resource, production service resource GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool function, protein, prediction, genome, annotation, gene, statistical analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: University of Dundee; Scotland; United Kingdom
Wellcome Trust 060269;
European Union fifth framework QLRI-CT-2000-00127
PMID:15550167 Free for academic use nlx_149269 http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html SCR_005790 2026-08-03 09:32:56 1
GoAnnotator
 
Resource Report
Resource Website
1+ mentions
GoAnnotator (RRID:SCR_005792) GOAnnotator data analysis service, service resource, analysis service resource, production service resource A tool for assisting the GO annotation of UniProt entries by linking the GO terms present in the uncurated annotations with evidence text automatically extracted from the documents linked to UniProt entries. Platform: Online tool text mining, protein, gene ontology, annotation is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: UniProt
has parent organization: University of Lisbon; Lisbon; Portugal
European Union contract QLRI-1999-50595 PMID:17181854 Free for academic use nlx_149303 SCR_005792 2026-08-03 09:32:56 1
GoPubMed
 
Resource Report
Resource Website
10+ mentions
GoPubMed (RRID:SCR_005823) GoPubMed service resource, data or information resource, database A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool other analysis, literature curation and exploration, gene ontology, pubmed, literature, bio.tools is listed by: OMICtools
is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
is related to: PubMed
has parent organization: Biotechnology Center of the TU Dresden
European Union IST-2004-506779 PMID:15980585 Free for academic use biotools:gopubmed, nlx_149328, OMICS_01183 https://bio.tools/gopubmed SCR_005823 2026-08-03 09:32:48 29
GOSlimViewer
 
Resource Report
Resource Website
10+ mentions
GOSlimViewer (RRID:SCR_005665) GOSlimViewer data analysis service, service resource, analysis service resource, production service resource Service to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs. agriculture, browser, slimmer-type tool, gene ontology, gene, ontology, ontology or annotation browser is listed by: Gene Ontology Tools
is listed by: OMICtools
is related to: Gene Ontology
has parent organization: AgBase
USDA ;
Mississippi State University; Mississippi; USA ;
MSU Office of Research ;
MSU Bagley College of Engineering ;
MSU College of College of Veterinary Medicine ;
MSU Life Science and Biotechnology Institute
PMID:17135208
PMID:16961921
Free for academic use nlx_149103, OMICS_02270 SCR_005665 GO Slim Viewer, GOSlim Viewer 2026-08-03 09:32:44 40
Expression Profiler
 
Resource Report
Resource Website
1+ mentions
Expression Profiler (RRID:SCR_005821) Expression Profiler data analysis service, service resource, analysis service resource, production service resource THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: European Bioinformatics Institute
European Union ;
Wellcome Trust ;
Estonian Science Foundation 5724;
Estonian Science Foundation 5722
PMID:15215431 THIS RESOURCE IS NO LONGER IN SERVICE biotools:expression_profiler, nlx_149323 https://bio.tools/expression_profiler SCR_005821 Expression Profiler at the EBI 2026-08-03 09:32:56 6
GOChase
 
Resource Report
Resource Website
1+ mentions
GOChase (RRID:SCR_005822) GOChase data analysis service, service resource, analysis service resource, production service resource GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations. # GOChase-History resolves the whole modification history of GO IDs. # GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks. # A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections. # When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. Platform: Online tool other analysis, historical views of go, gene ontology, annotation is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Seoul National University College of Medicine; Seoul; South Korea
Ministry of Health and Welfare - Republic of Korea 0405-BC0206040004 PMID:15513987 Free for academic use nlx_149324 SCR_005822 GOChase: correcting errors from gene ontology-based annotations for gene products 2026-08-03 09:32:56 1
SGD Gene Ontology Slim Mapper
 
Resource Report
Resource Website
10+ mentions
SGD Gene Ontology Slim Mapper (RRID:SCR_005784) GO Slim Mapper data analysis service, service resource, analysis service resource, production service resource The GO Slim Mapper (aka GO Term Mapper) maps the specific, granular GO terms used to annotate a list of budding yeast gene products to corresponding more general parent GO slim terms. Uses the SGD GO Slim sets. Three GO Slim sets are available at SGD: * Macromolecular complex terms: protein complex terms from the Cellular Component ontology * Yeast GO-Slim: GO terms that represent the major Biological Processes, Molecular Functions, and Cellular Components in S. cerevisiae * Generic GO-Slim: broad, high level GO terms from the Biological Process and Cellular Component ontologies selected and maintained by the Gene Ontology Consortium (GOC) Platform: Online tool gene, annotation, gene ontology, protein complex, biological process, molecular function, cellular component, gene ontology, orf, yeast, statistical analysis, slimmer-type tool, function is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: SGD
Free for academic use nlx_149258 SCR_005784 GO Term Mapper, Gene Ontology Slim Mapper 2026-08-03 09:32:56 31
GO-Module
 
Resource Report
Resource Website
1+ mentions
GO-Module (RRID:SCR_005813) GO-Module data analysis service, service resource, analysis service resource, production service resource GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool functional similarity, visualization, other analysis, reduce the dimensionality of go enrichment results, produce interpretable biomodules of significant go terms, gene ontology, ontology or annotation visualization, annotation is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: AmiGO
has parent organization: University of Illinois at Chicago; Illinois; USA
NIH ;
Cancer Research Foundation ;
NLM K22 LM008308;
NCI 1U54CA121852;
NCRR UL1 RR024999
PMID:21421553 Free for academic use nlx_149322 SCR_005813 Hierarchical optimization of enriched GO terms 2026-08-03 09:32:56 3
GOanna
 
Resource Report
Resource Website
10+ mentions
GOanna (RRID:SCR_005684) GOanna data analysis service, service resource, analysis service resource, production service resource GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database of GO annotated proteins. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match. Platform: Online tool agriculture, annotation, protein, ontology or annotation search engine, ontology or annotation editor is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: AgBase
USDA ;
Mississippi State University; Mississippi; USA ;
MSU Office of Research ;
MSU Bagley College of Engineering ;
MSU College of College of Veterinary Medicine ;
MSU Life Science and Biotechnology Institute
PMID:17135208
PMID:16961921
Free for academic use nlx_149139 SCR_005684 AgBase GOanna 2026-08-03 09:32:45 17
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products
 
Resource Report
Resource Website
FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products (RRID:SCR_005738) FuSSiMeG data analysis service, service resource, analysis service resource, production service resource FuSSiMeG is being discontinued, may not be working properly. Please use our new tool ProteinOn. Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins. Platform: Online tool protein, similarity, gene ontology, gene, ontology, statistical analysis, term enrichment, semantic similarity, analysis, other analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: ProteInOn
has parent organization: University of Lisbon; Lisbon; Portugal
Free for academic use nlx_149198 SCR_005738 Functional Semantic Similarity Measure between Gene-Products, Functional Semantic Similarity Measure between Gene Products (FuSSiMeG) 2026-08-03 09:32:55 0
Mouse Genome Informatics (MGI)
 
Resource Report
Resource Website
1000+ mentions
Mouse Genome Informatics (MGI) (RRID:SCR_006460) MGI data or information resource, database International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. RIN, Resource Information Network, molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standard, RRID Community Authority uses: InterMOD
is used by: NIF Data Federation
is used by: Resource Identification Portal
is used by: PhenoGO
is used by: Integrated Animals
is used by: Cytokine Registry
is used by: NIH Heal Project
is recommended by: Resource Identification Portal
is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: 3DVC
is listed by: re3data.org
is listed by: OMICtools
is listed by: NIH Data Sharing Repositories
is listed by: InterMOD
is listed by: Resource Information Network
is affiliated with: InterMOD
is related to: MONARCH Initiative
is related to: MouseCyc
is related to: AmiGO
is related to: Gene Expression Database
is related to: Bgee: dataBase for Gene Expression Evolution
is related to: HomoloGene
is related to: Rat Gene Symbol Tracker
is related to: Enhancer Trap Line Browser
is related to: Integrated Brain Gene Expression
is related to: MalaCards
is related to: Gene Ontology
is related to: BioMart Project
is related to: NIH Data Sharing Repositories
is related to: RIKEN integrated database of mammals
is related to: JAX Neuroscience Mutagenesis Facility
is related to: PhenoGO
is related to: International Mouse Strain Resource
is related to: Mouse Genome Database
is related to: Mouse Tumor Biology Database
has parent organization: Jackson Laboratory
is parent organization of: Anatomy of the Laboratory Mouse
is parent organization of: Mouse Genome Informatics Transgenes
is parent organization of: Federation of International Mouse Resources
is parent organization of: MGI GO Browser
is parent organization of: Recombinase (cre) Activity
is parent organization of: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project
is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource
is parent organization of: MGI strains
is parent organization of: MPO
is parent organization of: Phenotypes and Mutant Alleles
is parent organization of: Human Mouse Disease Connection
is parent organization of: Functional Annotation
is parent organization of: Strains, SNPs and Polymorphisms
is parent organization of: Vertebrate Homology
is parent organization of: Batch Data and Analysis Tool
is parent organization of: Nomenclature
NHGRI HG000330;
NHGRI HG002273;
NICHD HD033745;
NCI CA089713
PMID:19274630
PMID:18428715
Free, Freely available nif-0000-00096, OMICS_01656, r3d100010266 http://www.informatics.jax.org/batch, http://www.informatics.jax.org/submit.shtml, http://www.informatics.jax.org/expression.shtml, https://doi.org/10.17616/R35P54 SCR_006460 , MGI, Mouse Genome Informatics 2026-08-03 09:33:01 1119
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit
 
Resource Report
Resource Website
10+ mentions
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) GOEAST data analysis service, service resource, analysis service resource, production service resource Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) is a web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods. Compared with available GO analysis tools, GOEAST has the following unique features: * GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats. * GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy. * Note that GOEAST generates separate graph for each of the three GO categories, namely biological process, molecular function and cellular component. * GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis. Platform: Online tool statistical analysis, gene ontology, high-throughput, microarray, hybridization, gene, visualization, bio.tools is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: Chinese Academy of Sciences; Beijing; China
National Natural Science Foundation of China 30725014;
National Natural Science Foundation of China 90612019;
Ministry of Science and Technology of China 2007CB946901;
Chinese Academy of Sciences KSCX2-YW-R-134;
Chinese Academy of Sciences KSCX2-YW-N-024
PMID:18487275 Free for academic use biotools:goeast, nlx_149248 https://bio.tools/goeast SCR_006580 Gene Ontology Enrichment Analysis Software Toolkit, Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) 2026-08-03 09:33:04 38
GeneTerm Linker
 
Resource Report
Resource Website
1+ mentions
GeneTerm Linker (RRID:SCR_006385) GTLinker data analysis service, service resource, analysis service resource, production service resource Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service. gene, functional annotation, function, functional metagroup, p-value, annotation, web service is listed by: OMICtools
is related to: Gene Ontology
is related to: KEGG
is related to: InterPro
has parent organization: Spanish National Research Council; Madrid; Spain
PMID:21949701 Acknowledgement requested OMICS_02227 SCR_006385 GeneTerm Linker - post enrichment functional association by non-redundant reciprocal linkage 2026-08-03 09:33:06 2
GeneTrail
 
Resource Report
Resource Website
100+ mentions
GeneTrail (RRID:SCR_006250) GeneTrail data analysis service, service resource, analysis service resource, production service resource A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: KEGG
is related to: TRANSPATH
is related to: TRANSFAC
is related to: Gene Ontology
has parent organization: Saarland University; Saarbrucken; Germany
PMID:17526521 THIS RESOURCE IS NO LONGER IN SERVICE biotools:genetrail, OMICS_02236 https://bio.tools/genetrail SCR_006250 2026-08-03 09:33:02 106
Magic
 
Resource Report
Resource Website
500+ mentions
Magic (RRID:SCR_006406) MAGIC service resource, data or information resource, database Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. gene expression, microarray, development stage, annotation, line, perturbation, gene, contrast, pathway, locus tag, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Expression Omnibus
is related to: ArrayExpress
is related to: Plant Ontology
is related to: Gene Ontology
has parent organization: Ghent University; Ghent; Belgium
PMID:24407224 biotools:magic, OMICS_02206 https://bio.tools/magic SCR_006406 MAGIC - MAize Gene expressIon Compendium, MAize Gene expressIon Compendium 2026-08-03 09:33:04 706
GOnet
 
Resource Report
Resource Website
1+ mentions
GOnet (RRID:SCR_018977) web service, data access protocol, service resource, software resource Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools is listed by: Debian
is listed by: bio.tools
works with: Gene Ontology
NIH Common Fund ;
NIGMS ;
NHGRI R24 HG010032;
NIAID U19 AI118610;
NIAID U19 AI118626
PMID:30526489 biotools:GOnet https://github.com/mikpom/gonet, https://bio.tools/GOnet SCR_018977 2026-08-03 09:37:06 3

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