How To Download Ontology Data From Amigo

Knowledgebase for functions of genes and cistron products

The Gene Ontology

Content
Description	Resource with controlled vocabulary to depict the function of genes and gene products
Access
Website	geneontology.org

The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species.^[1] More than specifically, the projection aims to: i) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and digest and disseminate annotation data; and 3) provide tools for easy admission to all aspects of the information provided by the project, and to enable functional interpretation of experimental information using the Become, for case via enrichment analysis.^{[two] [iii]} Go is part of a larger classification effort, the Open Biomedical Ontologies, beingness 1 of the Initial Candidate Members of the OBO Foundry.^[4]

Whereas gene nomenclature focuses on factor and gene products, the Gene Ontology focuses on the function of the genes and gene products. The GO also extends the try by using markup linguistic communication to make the data (not merely of the genes and their products but also of curated attributes) machine readable, and to do and so in a way that is unified across all species (whereas cistron nomenclature conventions vary by biological taxon).

Terms and ontology [edit]

From a practical view, an ontology is a representation of something we know about. "Ontologies" consist of representations of things that are detectable or straight observable, and the relationships between those things. There is no universal standard terminology in biological science and related domains, and term usages may be specific to a species, research surface area or even a particular enquiry group. This makes communication and sharing of data more difficult. The Gene Ontology project provides an ontology of divers terms representing factor product properties. The ontology covers three domains:

• cellular component, the parts of a prison cell or its extracellular surroundings;
• molecular function, the elemental activities of a cistron production at the molecular level, such every bit binding or catalysis;
• biological procedure, operations or sets of molecular events with a defined start and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.

Each Get term inside the ontology has a term name, which may be a word or string of words; a unique alphanumeric identifier; a definition with cited sources; and an ontology indicating the domain to which information technology belongs. Terms may also have synonyms, which are classed as being exactly equivalent to the term name, broader, narrower, or related; references to equivalent concepts in other databases; and comments on term significant or usage. The GO ontology is structured equally a directed acyclic graph, and each term has defined relationships to one or more other terms in the same domain, and sometimes to other domains. The Go vocabulary is designed to be species-neutral, and includes terms applicable to prokaryotes and eukaryotes, single and multicellular organisms.

GO is not static, and additions, corrections and alterations are suggested by, and solicited from, members of the enquiry and annotation communities, as well every bit by those directly involved in the GO project.^[5] For example, an analyst may asking a specific term to represent a metabolic pathway, or a section of the ontology may exist revised with the help of community experts (east.g.^[half-dozen]). Suggested edits are reviewed past the ontology editors, and implemented where appropriate.

The Get ontology and annotation files are freely available from the Go website^[7] in a number of formats, or can be accessed online using the GO browser AmiGO. The Factor Ontology project also provides downloadable mappings of its terms to other nomenclature systems.

Example term [edit]

id: Get:0000016

name: lactase activity

ontology: molecular_function

def: "Catalysis of the reaction: lactose + H2o=D-glucose + D-galactose." [EC:3.2.1.108]

synonym: "lactase-phlorizin hydrolase activeness" BROAD [EC:three.2.ane.108]

synonym: "lactose galactohydrolase activeness" Exact [EC:3.2.1.108]

xref: EC:three.ii.ane.108

xref: MetaCyc:LACTASE-RXN

xref: Reactome:20536

is_a: GO:0004553 ! hydrolase action, hydrolyzing O-glycosyl compounds

Data source:^[viii]

Notation [edit]

Genome notation encompasses the practice of capturing data about a factor product, and GO annotations use terms from the Become to practise so. Annotations from Go curators are integrated and disseminated on the GO website, where they can be downloaded straight or viewed online using AmiGO.^[ix] In improver to the factor production identifier and the relevant GO term, Get annotations have at to the lowest degree the following data: The reference used to make the annotation (e.g. a journal article); An bear witness code denoting the type of bear witness upon which the annotation is based; The date and the creator of the annotation

Supporting information, depending on Get term and prove used and supplementary data, such every bit the conditions the part is observed under, may as well exist included in a GO annotation.

The evidence code comes from a controlled vocabulary of codes, the Show Code Ontology, covering both manual and automatic note methods.^[10] For example, Traceable Author Statement (TAS) means a curator has read a published scientific paper and the metadata for that annotation bears a citation to that paper; Inferred from Sequence Similarity (ISS) means a man curator has reviewed the output from a sequence similarity search and verified that information technology is biologically meaningful. Annotations from automated processes (for example, remapping annotations created using some other annotation vocabulary) are given the lawmaking Inferred from Electronic Notation (IEA). In 2010, over 98% of all Become annotations were inferred computationally, not by curators, but every bit of July ii, 2019, only about 30% of all GO annotations were inferred computationally.^{[11] [12]} Every bit these annotations are non checked by a human, the GO Consortium considers them to be marginally less reliable and they are commonly to higher level, less detailed terms. Full annotation data sets can be downloaded from the Get website. To support the evolution of note, the Go Consortium provides workshops and mentors new groups of curators and developers.

Many machine learning algorithms have been designed and implemented to predict Gene Ontology annotations.^{[13] [14]}

Example annotation [edit]

Gene product: Actin, alpha cardiac muscle 1, UniProtKB:P68032

GO term: heart contraction ; Go:0060047 (biological procedure)

Evidence code: Inferred from Mutant Phenotype (IMP)

Reference: PMID 17611253

Assigned by: UniProtKB, June 6, 2008

Information source:^[15]

Tools [edit]

There are a large number of tools available^[sixteen] both online and to download that apply the data provided by the Go projection. The vast majority of these come from 3rd parties; the Go Consortium develops and supports two tools, AmiGO and OBO-Edit.

AmiGO^{[17] [9]} is a web-based awarding that allows users to query, scan and visualize ontologies and cistron production notation information. Information technology also has a BLAST tool,^[18] tools allowing analysis of larger data sets,^{[19] [twenty]} and an interface to query the Become database directly.^[21]

AmiGO tin can exist used online at the GO website to admission the data provided by the GO Consortium, or can exist downloaded and installed for local use on any database employing the GO database schema (e.g.^[22]). It is gratuitous open source software and is available every bit part of the go-dev software distribution.^[23]

OBO-Edit^[24] is an open up source, platform-independent ontology editor developed and maintained by the Gene Ontology Consortium. It is implemented in Coffee, and uses a graph-oriented approach to display and edit ontologies. OBO-Edit includes a comprehensive search and filter interface, with the selection to return subsets of terms to make them visually distinct; the user interface tin likewise be customized according to user preferences. OBO-Edit also has a reasoner that can infer links that have non been explicitly stated, based on existing relationships and their backdrop. Although it was adult for biomedical ontologies, OBO-Edit can be used to view, search and edit whatsoever ontology. It is freely available to download.^[23]

Consortium [edit]

The Cistron Ontology Consortium is the gear up of biological databases and research groups actively involved in the factor ontology project.^[12] This includes a number of model organism databases and multi-species protein databases, software development groups, and a dedicated editorial role.

History [edit]

The Cistron Ontology was originally constructed in 1998 by a consortium of researchers studying the genomes of three model organisms: Drosophila melanogaster (fruit fly), Mus musculus (mouse), and Saccharomyces cerevisiae (brewer's or bakery's yeast).^[25] Many other Model Organism Databases have joined the Cistron Ontology Consortium, contributing not only annotation information, but also contributing to the evolution of the ontologies and tools to view and utilise the information. Many major establish, animal and microorganism databases make a contribution towards this project.^[7] Every bit of July 2019, the GO contains 44,945 terms; there are 6,408,283 annotations to 4,467 different biological organisms.^[7] In that location is a significant body of literature on the development and employ of the GO, and it has become a standard tool in the bioinformatics arsenal. Their objectives take three aspects: building gene ontology, assigning ontology to gene/cistron products and developing software and databases for the commencement 2 objects.

Several analyses of the Gene Ontology using formal, domain-contained properties of classes (the metaproperties) are also starting to announced. For instance, an ontological analysis of biological ontologies see.^[26]

Encounter also [edit]

• Blast2GO
• Comparative Toxicogenomics Database
• DAVID bioinformatics
• Interferome
• National Center for Biomedical Ontology
• Disquisitional Assessment of Function Notation

References [edit]

1. ^ The Gene Ontology Consortium (January 2008). "The Gene Ontology project in 2008". Nucleic Acids Research. 36 (Database upshot): D440–4. doi:ten.1093/nar/gkm883. PMC2238979. PMID 17984083.
2. ^ Dessimoz, Christophe; Škunca, Nives, eds. (2017). The Factor Ontology Handbook. Methods in Molecular Biological science. Vol. 1446. doi:10.1007/978-1-4939-3743-1. ISBN9781493937431. ISSN 1064-3745. S2CID 3708801.
3. ^ Gaudet, Pascale; Škunca, Nives; Hu, James C.; Dessimoz, Christophe (2017). "Primer on the Factor Ontology". The Gene Ontology Handbook. Methods in Molecular Biology. Vol. 1446. pp. 25–37. doi:10.1007/978-1-4939-3743-1_3. ISBN978-ane-4939-3741-7. ISSN 1064-3745. PMC6377150. PMID 27812933.
4. ^ Smith B, Ashburner Thousand, Rosse C, Bard J, Issues W, Ceusters Due west, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S (November 2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical information integration". Nature Biotechnology. 25 (11): 1251–five. doi:x.1038/nbt1346. PMC2814061. PMID 17989687.
5. ^ Lovering, Ruth C. (2017). "How Does the Scientific Community Contribute to Factor Ontology?". In Dessimoz, C; Skunca, N (eds.). The Gene Ontology Handbook. Methods in Molecular Biology. Vol. 1446. Springer (New York). pp. 85–93. doi:10.1007/978-1-4939-3743-1_7. ISBN978-1-4939-3741-7. ISSN 1064-3745. PMID 27812937.
6. ^ Diehl AD, Lee JA, Scheuermann RH, Blake JA (April 2007). "Ontology development for biological systems: immunology". Bioinformatics. 23 (7): 913–5. doi:10.1093/bioinformatics/btm029. PMID 17267433.
7. ^ ^{a b c} "The Gene Ontology Resource". Gene Ontology Consortium.
8. ^ Sjcarbon,Factor Ontology Consortium Wiki (2013-07-x). "AmiGO_2_Manual:term_Page" (html).
9. ^ ^{a b} AmiGO--the current official web-based set of tools for searching and browsing the Gene Ontology database
10. ^ "Evidence Code Ontology". Testify Code Ontology.
11. ^ du Plessis L, Skunca N, Dessimoz C (November 2011). "The what, where, how and why of cistron ontology--a primer for bioinformaticians". Briefings in Bioinformatics. 12 (6): 723–35. doi:10.1093/bib/bbr002. PMC3220872. PMID 21330331.
12. ^ ^{a b} "The GO Consortium". Retrieved 2009-03-sixteen .
13. ^ Pinoli P, Chicco D, Masseroli Chiliad (June 2013). "Computational algorithms to predict Cistron Ontology annotation". BMC Bioinformatics. 16 (6): S4. doi:ten.1186/1471-2105-16-S6-S4. PMC4416163. PMID 25916950.
14. ^ Cozzetto, Domenico; Jones, David T. (2017). "Computational Methods for Annotation Transfers from Sequence". In Dessimoz, C; Skunca, Northward (eds.). The Gene Ontology Handbook. Methods in Molecular Biology. Vol. 1446. Springer (New York). pp. 55–67. doi:x.1007/978-i-4939-3743-1_5. ISBN978-1-4939-3741-vii. ISSN 1064-3745. PMID 27812935.
15. ^ The GO Consortium (2009-03-sixteen). "AmiGO: P68032 Associations".
16. ^ Mosquera JL, Sánchez-Pla A (July 2008). "SerbGO: searching for the all-time Get tool". Nucleic Acids Research. 36 (Web Server issue): W368–71. doi:10.1093/nar/gkn256. PMC2447766. PMID 18480123.
17. ^ Carbon Due south, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S (January 2009). AmiGO Hub; Web Presence Working Group. "AmiGO: online access to ontology and annotation information". Bioinformatics. 25 (2): 288–9. doi:10.1093/bioinformatics/btn615. PMC2639003. PMID 19033274.
18. ^ "AmiGO Blast tool". Archived from the original on 2011-08-twenty. Retrieved 2009-03-13 .
19. ^ AmiGO Term Enrichment tool Archived 2008-04-07 at the Wayback Machine; finds meaning shared Become terms in an annotation gear up
20. ^ AmiGO Slimmer Archived 2011-09-29 at the Wayback Machine; maps granular annotations up to high-level terms
21. ^ GOOSE, Become Online SQL Environment; allows straight SQL querying of the GO database
22. ^ The Plant Ontology Consortium (2009-03-16). "Plant Ontology Consortium". Retrieved 2009-03-16 .
23. ^ ^{a b} "Gene Ontology downloads at SourceForge". Retrieved 2009-03-16 .
24. ^ Solar day-Richter J, Harris MA, Haendel M, Lewis S (August 2007). "OBO-Edit--an ontology editor for biologists". Bioinformatics. 23 (sixteen): 2198–200. doi:10.1093/bioinformatics/btm112. PMID 17545183.
25. ^ Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Red JM, Davis AP, Dolinski 1000, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (May 2000). "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics. 25 (1): 25–ix. doi:x.1038/75556. PMC3037419. PMID 10802651.
26. ^ Deb, B. (2012). "An ontological analysis of some biological ontologies". Frontiers in Genetics. iii: 269. doi:10.3389/fgene.2012.00269. PMC3509948. PMID 23226158.

External links [edit]

• AmiGO - the current official web-based set of tools for searching and browsing the Gene Ontology database
• Factor Ontology Consortium - official site
• PlantRegMap - Get notation for 165 institute species and Become enrichment Analysis

Source: https://en.wikipedia.org/wiki/Gene_ontology

Posted by: blanchettemajoys.blogspot.com

Share this post