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Cellular Component Ontology Guidelines

The cellular component ontology describes locations, at the levels of subcellular structures and macromolecular complexes. Examples of cellular components include 'nuclear inner membrane', with the synonym 'inner envelope', and the 'ubiquitin ligase complex', with several subtypes of these complexes represented.

Species-Specific Terms

Handling Species Specificity

One of the biggest problems for a controlled vocabulary is choosing term names and definitions that will unambiguously identify a component, function or process. If a word or phrase refers to different entities or processes depending upon the organism, subclasses are created based on differentiating characteristics, such structure, physical composition or order of subprocesses, rather than by identifying the taxonomic group in which the component or process occurs.

Scratch

This is a scratch page for people to try things out on. Please don't erase this message. foo@bar.com

GO File Format Guide

GO Formats

The GO File Format Guide documents the structure and syntax of the files available on the GO website, to assist users who need to read, write parsers for, or create these files. The following file formats are documented separately:

Annotation

Annotation is the process of assigning GO terms to gene products. The annotation data in the GO database is contributed by members of the GO Consortium, and the Consortium is continuously encouraging new groups to start contributing their annotations. The list of links below offer details on the GO annotation policies and the annotation process, as well as direct users to other pages of interest on GO annotation conventions, the standard operating procedures used by some consortium members, and the GO annotation file format guide.

Ontology Documentation

The Gene Ontology defines the universe of concepts relating to gene functions (‘GO terms’), and how these functions are related to each other (‘relations’). It is constantly revised and expanded as biological knowledge accumulates.

About

The Gene Ontology Project

Introduction to the GO resource

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. The structured knowledge in the ontology is a crucial part of the global biomedical informatics infrastructure.

Guide to GO Evidence Codes

A GO annotation consists of a GO term associated with a specific reference that describes the work or analysis upon which the association between a specific GO term and gene product is based. Each annotation must also include an evidence code to indicate how the annotation to a particular term is supported. Although evidence codes do reflect the type of work or analysis described in the cited reference which supports the GO term to gene product association, they are not necessarily a classification of types of experiments/analyses.

ID Mapping Files

ID Mapping Files

This page documents the file formats used to store the mapping between the Database object IDs to corresponding sequence IDs in UniProtKB or NCBI.
  • gp2protein file
  • gp2rna file
  • gp_unlocalized

gp2protein file

A gp2protein file is a tab-delimited file that provides a mapping between database object IDs and protein sequence IDs. gp2protein files contributed by annotation groups are available for download.

Need for gp2protein file