The Sequence Ontology: a tool for the unification of genome annotations
Open accessAbstract
The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
BioPAX reuses standard controlled vocabularies, including Gene Ontology for cellular location, PSI-MI vocabularies for evidence codes and interaction types, and Sequence Ontology for sequence regions.
“BioPAX reuses a number of standard controlled vocabularies defined by other groups. For example, Gene Ontology40 is used to describe cellular location, PSI-MI vocabularies38 are used to define evidence codes, experimental forms, interaction types, relationship types and sequence modifications, and Sequence Ontology41 is used to define types of sequence regions, such as a promoter region on DNA in”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [41]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Alberts, B., Johnson, A., Lewis, J. H., Morgan, D. O., RAFF, M. C., Roberts, K. J., & Walter, P. (2017) · W.W. Norton eBooks · doi:10.1201/9781315735368 · Cited by 7,937 · see citing works
The Bioperl Toolkit: Perl Modules for the Life SciencesPreprint
Stajich, J., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I. F., Lapp, H., et al. (2002) · Genome Research · doi:10.1101/gr.361602 · Cited by 1,642 · see citing works
Self-citationThe EMBL Nucleotide Sequence Database
Baker, W. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.19 · Cited by 1,107 · see citing works
Lewis, B. P., Green, R. E., & Brenner, S. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0136770100 · Cited by 1,049 · see citing works
Relations in biomedical ontologies
Smith, B., Ceusters, W. M., Klagges, B. R. E., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A. L., & Rosse, C. (2005) · Genome biology · doi:10.1186/gb-2005-6-5-r46 · Cited by 1,030 · see citing works
Self-citationSIMONS, P. M. (1987) · DIAL (Catholic University of Leuven) · doi:10.1093/acprof:oso/9780199241460.001.0001 · Cited by 978 · see citing works
A Taxonomy of Part‐Whole Relations
Winston, M. E., Chaffin, R. J. S., & Herrmann, D. J. (1987) · Cognitive Science · doi:10.1207/s15516709cog1104_2 · Cited by 971 · see citing works
Creating the Gene Ontology Resource: Design and ImplementationPreprint
The Gene Ontology Consortium (2001) · Genome Research · doi:10.1101/gr.180801 · Cited by 957 · see citing works
Rhee, S. Y. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg076 · Cited by 921 · see citing works
Creating the gene ontology resource: design and implementation.
Blake, J. A., Corradi, J., Eppig, J. T., Hill, D. P., Richardson, J. E., & Ringwald, M. (2001) · The Mouseion at the JAXlibrary (Jackson Laboratory) · Cited by 826 · see citing works
Mays, W. (1971) · Philosophical Books · doi:10.1111/j.1468-0149.1971.tb00536.x · Cited by 805 · see citing works
MOLECULAR BIOLOGY OF THE CELL, 5TH EDITION
Fenderson, B. A. (2008) · Shock · doi:10.1097/01.shk.0000286288.33338.f6 · Cited by 605 · see citing works
Annotation of the Drosophila melanogastereuchromatic genome: a systematic review
Misra, S., Crosby, M. A., Mungall, C., Matthews, B. B., Campbell, K. S., Hradecky, P., Huang, Y., Kaminker, J. S., Millburn, G., Prochnik, S. E., et al. (2002) · Genome biology · doi:10.1186/gb-2002-3-12-research0083 · Cited by 376 · see citing works
Self-citationA formal definition of binary topological relationships
Egenhofer, M. J. (1989) · Lecture notes in computer science · doi:10.1007/3-540-51295-0_148 · Cited by 345 · see citing works
WormBase: network access to the genome and biology of Caenorhabditis elegans
Stein, L. D. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.82 · Cited by 328 · see citing works
Self-citationThe EMBL Nucleotide Sequence Database
Kulikova, T. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh120 · Cited by 166 · see citing works
The Drosophila melanogaster Genome
Lasko, P. F. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.150.2.f51 · Cited by 141 · see citing works
The Drosophila Melanogaster Genome
Celniker, S., & Rubin, G. M. (2003) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.4.070802.110323 · Cited by 133 · see citing works
Saccharomyces genome database: Underlying principles and organisation
Dwight, S. S. (2004) · Briefings in Bioinformatics · doi:10.1093/bib/5.1.9 · Cited by 97 · see citing works
DDBJ in the stream of various biological data
Miyazaki, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh127 · Cited by 93 · see citing works
Hanke, P. D., & Storti, R. V. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.9.3591 · Cited by 84 · see citing works
An integrated computational pipeline and database to support whole-genome sequence annotation
Mungall, C., Misra, S., Berman, B. P., et al. (2002) · Genome biology · doi:10.1186/gb-2002-3-12-research0081 · Cited by 53 · see citing works
Self-citationHanke, P. D., & Storti, R. V. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.9.3591-3602.1988 · Cited by 22 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Cruse DA Lexical Semantics 1986 Cambridge, UK: Cambridge University Press
Cited by
Sorted by citations
Gene Ontology Consortium: going forward
The Gene Ontology Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1179 · Cited by 3,492 · see citing works
Large-scale whole-genome sequencing of the Icelandic population
Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A., Besenbacher, S., Magnusson, G., Halldorsson, B. V., Hjartarson, E., et al. (2015) · Nature Genetics · doi:10.1038/ng.3247 · Cited by 791 · see citing works
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · see citing works
“For example, Gene Ontology 40 is used to describe cellular location, PSI-MI vocabularies 38 are used to define evidence codes, experimental forms, interaction types, relationship types and sequence modifications, and Sequence Ontology 41 is used to define types of sequence regions, such as a promoter region on DNA inv…”
Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3774 · Cited by 628 · see citing works
LNCipedia 5: towards a reference set of human long non-coding RNAs
Volders, P.-J., Anckaert, J., Verheggen, K., Nuytens, J., Martens, L., Mestdagh, P., & Vandesompele, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1031 · Cited by 547 · see citing works
Genome Project Standards in a New Era of Sequencing
Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., et al. (2009) · Science · doi:10.1126/science.1180614 · Cited by 400 · see citing works
Rfam: Wikipedia, clans and the “decimal” release
Gardner, P. P., Daub, J., Tate, J., Moore, B. L., Osuch, I. H., Griffiths-Jones, S., Finn, R. D., Nawrocki, E. P., Kolbe, D. L., Eddy, S. R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1129 · Cited by 390 · see citing works
PomBase: a comprehensive online resource for fission yeast
Wood, V., Harris, M. A., McDowall, M. D., Rutherford, K., Vaughan, B. W., Staines, D. M., Aslett, M., Lock, A., Bahler, J., Kersey, P. J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr853 · Cited by 321 · see citing works
Identification of a large set of rare complete human knockouts
Sulem, P., Helgason, H., Oddson, A., Stefansson, H., Gudjonsson, S. A., Zink, F., Hjartarson, E., Sigurdsson, G. T., Jonasdottir, A., Jonasdottir, A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3243 · Cited by 220 · see citing works
Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP
Thormann, A., Halachev, M., McLaren, W., Moore, D. J., Svinti, V., Campbell, A., Kerr, S. M., Tischkowitz, M., Hunt, S. E., Dunlop, M. G., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10016-3 · Cited by 151 · see citing works
Sherman, D. J., Martin, T., Nikolski, M., Cayla, C., Souciet, J.-L., & Durrens, P. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn859 · Cited by 129 · see citing works
Morales, A., Kinnamon, D. D., Jordan, E., Platt, J., Vatta, M., Dorschner, M. O., Starkey, C. A., Mead, J. O., Ai, T., Burke, W., et al. (2020) · Circulation: Genomic and Precision Medicine · doi:10.1161/circgen.119.002480 · Cited by 114 · see citing works
Integrating biological data – the Distributed Annotation System
Jenkinson, A. M., Albrecht, M., Birney, E., Blankenburg, H., Down, T., Finn, R. D., Hermjakob, H., Hubbard, T. J., Jimenez, R. C., Jones, P., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-s8-s3 · Cited by 100 · see citing works
“In addition, a Protein Feature Ontology has been developed to fulfil a desire to constrain data to a controlled vocabulary so that it may be treated in a more intelligent manner.”
BackgroundInfluentialSemantic Web meets Integrative Biology: a survey
Chen, H., Yu, T., & Chen, J. Y. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs014 · Cited by 65 · see citing works
Stein, D., Kars, M. E., Wu, Y., Bayrak, Ç. S., Stenson, P. D., Cooper, D. N., Schlessinger, A., & Itan, Y. (2023) · Genome Medicine · doi:10.1186/s13073-023-01261-9 · Cited by 53 · see citing works
An ontology-based knowledge graph for representing interactions involving RNA molecules
Cavalleri, E., Cabri, A., Soto-Gomez, M., Bonfitto, S., Perlasca, P., Gliozzo, J., Callahan, T. J., Reese, J., Robinson, P. N., Casiraghi, E., et al. (2024) · Scientific Data · doi:10.1038/s41597-024-03673-7 · Cited by 33 · see citing works
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database
Hayman, G. T., Laulederkind, S. J. F., Smith, J. R., Wang, S.-J., Petri, V., Nigam, R., Tutaj, M., De Pons, J., Dwinell, M. R., & Shimoyama, M. (2016) · Database · doi:10.1093/database/baw034 · Cited by 27 · see citing works
- Authors
- Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., & Ashburner, M.
- Affiliations
- University of California, Berkeley (US)
- Cold Spring Harbor Laboratory (US)
- Wellcome Sanger Institute (GB)
- University of Cambridge (GB)
- Corresponding author
- Ashburner, Michael
- Venue
- Genome Biology
- Published
- 2005-04-29
- Volume
- 6
- Issue
- 5
- Pages
- R44-R44
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC1175956
- OpenAlex
- W2123171788
- Cited by
- 806
- References
- 24
- Citations by year
- 2026: 19 · 2025: 26 · 2024: 34 · 2023: 34 · 2022: 27 · 2021: 50 · 2020: 46 · 2019: 49 · 2018: 40 · 2017: 53 · 2016: 44 · 2015: 60 · 2014: 36 · 2013: 32 · 2012: 48
- FWCI
- 11.29
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
- Keywords
- Sequence Ontology, genome annotation, controlled vocabulary, part-whole relations, mereology, sequence features, annotation interoperability, automated reasoning
- MeSH terms
- Documentation, Exons, Terminology as Topic, RNA, Messenger, Software Design, Alternative Splicing, Vocabulary, Controlled, Computational Biology, Genomics, Databases, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
