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Project description

The ProThesaurus-Wiki is a thesaurus for gene and protein names. It is maintained by the Teaching and Research Unit Bioinformatics at the LMU.

The individual pages contain the following information:

• official gene and protein names
• synonyms and spelling variants including the sources (i.e. databases) for each synonym
• database identifier
• cross references to databases
• Gene Ontology annotations including the sources (i.e. databases) and evidence codes for each GO annotation
• a link for searching all synonyms for a given gene via PubMed or Google.

For examples, see e.g. TIMP4, MMP9 or FIG4. Please refer to the Help for information on how to search the ProThesaurus-Wiki, and use the Search page to find the genes/proteins you are interested in.

In addition to the protein/gene pages there is a category page for each GO term which contains:

• parent categories (i.e. parent GO terms)
• subcategories (i.e. child GO terms)
• part of-relations
• pages in this category (i.e. annotated genes/proteins)
• comments
• cross references
• synonyms

For examples, see e.g. GO:0005604 or GO:0019825.

The protein names within this thesaurus are regularly updated with information extracted from popular online databases. However, only after an extensive automatic curation procedure they are published in this Wiki. In addition, the readers are encouraged to suggest corrections to this thesaurus, e.g. additional synonyms. A description of how to participate in the improvement of this thesaurus is given here.

Please notice, that commercial use of the ProThesaurus-Wiki is not allowed. We also forbid the (partly or completely) download of the ProThesaurus data using automatic extraction methods. Please use the ProThesaurus web service or the ProTag client application in your custom software solutions. If you are interested in a cooperation please contact us. The full terms of use can be read here.

Publications

If you refer to the ProThesaurus-Wiki in your publications, please cite the following paper:

[1] Katrin Fundel and Ralf Zimmer: Gene and protein nomenclature in public databases, BMC Bioinformatics 2006, 7:372

See also External links.

News:

06/20/2006

The new release adds evidences for synonyms and GO annotations. The GO annotations contain the GO identifier, the GO term, the source (database and accession number) of the annotation and the GO evidence code. In addition, the Wiki now offers for each GO term a category page which lists the associated informations to the GO term, e.g. the parent categories, the synonyms, cross references, etc.

04/10/2006

Updated the synonym lists. The new release adds GO annotations.

01/12/2006

Initial import of the synonym lists for the organisms Fly, Human, Mouse, Rat and Yeast. This release includes database identifiers for the online databases FlyBase, HUGO, Entrez Gene, MGI, RGD, SGD and Swiss-Prot.