How to cite this record FAIRsharing.org: SO; Sequence Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6bc7h9; Last edited: March 13, 2019, 10:35 a.m.; Last accessed: Nov 17 2019 8:52 p.m.
Publication for citation The Sequence Ontology: a tool for the unification of genome annotations. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M.; Genome Biology ; 2005; 10.1186/gb-2005-6-5-r44;
Record updated: March 13, 2019, 10:22 a.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.6bc7h9' by 'The FAIRsharing Team' at 10:22, 13 Mar 2019 (approved): 'organizations' has been modified: Before: U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds SO administrators|http://www.sequenceontology.org/|Maintains After: U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds SO administrators|http://www.sequenceontology.org/|Maintains Department of Human Genetics, University of Utah, USA|http://www.genetics.utah.edu/|Maintains Added: Department of Human Genetics, University of Utah, USA|http://www.genetics.utah.edu/|Maintains Removed: 'supportLinks' has been modified: Before: firstname.lastname@example.org mailing list|http://sourceforge.net/p/song/mailman/ online documentation|http://www.sequenceontology.org/so_wiki/index.php/Main_Page online documentation|http://www.sequenceontology.org/resources/guide.html After: forum|https://github.com/The-Sequence-Ontology/SO-Ontologies/issues mailing email@example.com online documentation|http://www.sequenceontology.org/so_wiki/index.php/Main_Page online documentation|https://github.com/The-Sequence-Ontology/SO-Ontologies Added: forum|https://github.com/The-Sequence-Ontology/SO-Ontologies/issues mailing firstname.lastname@example.org online documentation|https://github.com/The-Sequence-Ontology/SO-Ontologies Removed: email@example.com mailing list|http://sourceforge.net/p/song/mailman/ online documentation|http://www.sequenceontology.org/resources/guide.html 'description' has been modified: Before: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. After: SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. The Sequence Ontology is a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence. 'licences' has been modified: Before: After: Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data Added: Creative Commons Attribution 4.0 International (CC BY 4.0)|https://creativecommons.org/licenses/by/4.0/|Data Removed: 'onto_disciplines' has been modified: Before: Life Sciences After: Bioinformatics Biology Life Sciences Added: Bioinformatics Biology Removed: 'dataProcesses' has been modified: Before: After: Download (OWL) Browse SO Added: Download (OWL) Browse SO Removed: 'onto_domains' has been modified: Before: deoxyribonucleic acid gene genome ribonucleic acid sequence_feature After: Sequence Sequence annotation deoxyribonucleic acid gene genome ribonucleic acid sequence_feature Added: Sequence Sequence annotation Removed:
Edits to 'https://fairsharing.org/FAIRsharing.6bc7h9' by 'The FAIRsharing Team' at 07:50, 01 Aug 2018 (approved): 'related_standards' has been modified: Before: Ontology for Genetic Interval Generic Feature Format Version 3 Fungal Gross Anatomy Ontology Fission Yeast Phenotype Ontology MicroArray Gene Expression Tabular Format After: Ontology for Genetic Interval Generic Feature Format Version 3 Fungal Gross Anatomy Ontology Fission Yeast Phenotype Ontology MicroArray Gene Expression Tabular Format CHADO XML Added: CHADO XML Removed:
Edits to 'https://fairsharing.org/FAIRsharing.6bc7h9' by 'The FAIRsharing Team' at 23:09, 15 Jul 2018 (approved): 'related_standards' has been modified: Before: bsg-s000091|Ontology for Genetic Interval bsg-s000235|Generic Feature Format Version 3 bsg-s002605|Fungal Gross Anatomy Ontology bsg-s000291|Fission Yeast Phenotype Ontology After: bsg-s000091|Ontology for Genetic Interval bsg-s000235|Generic Feature Format Version 3 bsg-s002605|Fungal Gross Anatomy Ontology bsg-s000291|Fission Yeast Phenotype Ontology bsg-s000080|MicroArray Gene Expression Tabular Format Added: bsg-s000080|MicroArray Gene Expression Tabular Format Removed:
Edits to 'https://fairsharing.org/FAIRsharing.6bc7h9' by 'The FAIRsharing Team' at 10:40, 11 Oct 2016 (approved): 'homepage' has been modified: Before: http://purl.bioontology.org/ontology/SO After: http://www.sequenceontology.org/
|forum||GitHub Issue Tracker|
|Mailing List||SO Mailing list|
|online documentation||SO Wiki Pages|
|online documentation||GitHub Repository|
|Contact||Karen Eilbeck ORCID|
No XSD schemas defined
Conditions of UseApplies to: Data use
The Sequence Ontology: a tool for the unification of genome annotations.
Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M.
Genome Biology 2005
Evolution of the Sequence Ontology terms and relationships.
Mungall CJ, Batchelor C, Eilbeck K.
J Biomed Inform. 2010
No guidelines defined
Models and Formats
No identifier schema standards defined
No metrics standards defined
Community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.
Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs.
Fungal and Oomycete genomics resource
FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.
modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.
Saccharomyces Genome Database
The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae. SGD contains a variety of biological information and tools with which to search and analyze it.
The Arabidopsis Information Resource
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets.
Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis
The UCSC Archaeal Genome Browser
The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.
WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.
Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.
Daphnia Water Flea Genome Database
wFleaBase includes data from all species of the genus, yet the primary species are Daphnia pulex and Daphnia magna, because of the broad set of genomic tools that have already been developed for these animals.
Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.
VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for 38 organisms including Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. Recent additions include large scale variant (SNP) datasets and population genetics data (genotype/phenotype).
European Variation Archive
The European Variation Archive is an open-access archive that accepts submission of, and provides access to, all types of genetic variation data from all species. All users are able to download any dataset, or query our study catalogue via our variation table. Access to EVA data is also provided by RESTful web services for a variety of applications, such as annotation pipelines.
MouseMine @ MGI
A database of integrated mouse data from MGI, powered by InterMine. MouseMine is member of InterMOD, a consortium of model organism databases dedicated to making cross-species data analysis easier through ongoing coordination and collaborative system development.
ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible.
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.
dictyBase is a single-access database for the complete genome sequence and expression data of four Dictyostelid species providing information on research, genome and annotations. There is also a repository of plasmids and strains held at the Dicty Stock Centre. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses.
Open Targets is a data integration platform for access to and visualisation of potential drug targets associated with disease. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources.
The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).
Hardwood Genomics Project
The Hardwood Genomics Project is a databases for expressed genes, genetic markers, genetic linkage maps, and reference populations. It provides lasting genomic and biological resources for the discovery and conservation of genes in hardwood trees for growth, adaptation and responses to environmental stresses such as drought, heat, insect pests and disease. All original sequence data is being deposited in NCBI's Sequence Read Archive and the genetic linkage maps and associated marker data will be available at the Dendrome database.
The Target-Pathogen database is a bioinformatic approach to prioritize drug targets in pathogens. Available genomic data for pathogens has created new opportunities for drug discovery and development, including new species, resistant and multiresistant ones. However, this data must be cohesively integrated to be fully exploited and be easy to interrogate. Target-Pathogen has been designed and developed as an online resource to allow genome wide based data consolidation from diverse sources focusing on structural druggability, essentiality and metabolic role of proteins. By allowing the integration and weighting of this information, this bioinformatic tool aims to facilitate the identification and prioritization of candidate drug targets for pathogens. With the structurome and drugome information Target-Pathogen is a unique resource to analyze whole genomes of relevants pathogens.
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
Huanglongbing (HLB) is a tritrophic disease complex involving citrus host trees, the Asian citrus psyllid (ACP) insect and a phloem restricted, bacterial pathogen Candidatus Liberibacter asiaticus (CLas). HLB is considered to be the most devastating of all citrus diseases, and there is currently no adequate control strategy. Citrusgreening.org is a database for host, vector and pathogen involved in citrus greening disease.
LNCipedia is a database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria.
BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-curated data sets to be applied to ruminants using orthology.
CHOmine integrates many types of data for Cricetulus griseus, and CHO cells. You can run flexible queries, export results and analyse lists of data.
Agronomic Linked Data
The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RDF knowledge base of 100M triples created by annotating and integrating more than 50 datasets from 10 data sources and linked using 10 ontologies.
Scroll for more...
This record is not implemented by any policy.
This record is maintained by keilbeck
U.S. National Library of Medicine (Government body)
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)
SO administrators (Consortium) Lead
1RC2HG005619 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
2R44HG002991 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
2R44HG003667 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
5R01HG004341 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
HG004341 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)
P41HG002273 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)