Annotation: linking literature to gene products

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Presentation transcript:

Annotation: linking literature to gene products How to find existing annotation for gene products and identify literature containing unannotated data.

Functional Annotation: linking literature to genes Genomic Annotation and Functional Modeling Workshop Maxwell H. Gluck Equine Research Center 15-16 November, 2011

Identifying functional literature. GO Browsers & databases display links to papers, where these are used to make the annotation (direct, experimental evidence codes). However, annotation lags publication: how to find functional papers? UniProtKB links Entrez Gene links & GeneRIFs PubMed & GOPubMed

Note – for many un-reviewed or un-annotated UniProt records, the references section is incomplete and likely has references to do with structural annotation (no functional data).

PubMed link Links out to PubMed records. Note that links are to PubMed records that are curated to this gene - may be incomplete - may be incorrect (text mining – e.g. ovalbumin reagent)

GeneRIFs “Gene References Into Function”. References are linked to this page by researchers! - simple, easy to use - may be incomplete

Finding unlinked publications. Targeted PubMed searches Gene name(s), gene symbol, protein name(s) Limit by species (using species name OR MeSH terms)

Now what??

Functional Literature Triage PubMed searches: Cellular component: e.g. “subcellular localization” Molecular function: e.g. activity, binding, assay, interaction Biological Process: e.g. pathway, developmental process. Sequence based papers – limited use for function Tissue expression – limited only to active molecule (protein, noncoding RNA – not mRNA in situ hybridization) Functional information not always found in abstract!

OVA used as a reagent (to test Tcell development). - only incidental to OVA function

OVA mentioned as part of introduction to serpins. OVA = SERPINB14 but paper is about SERPINB11.

OVA regulated by steroid hormones – biological process? OVA secreted – cellular component?

http://www.gopubmed.org GOPubMed: Uses the PubMed database (note number of papers are the same for the same search. Incorporates MeSH & GO term text mining to try and identify most relevant searches. Note: errors in text mining!

Use links on the side to identify papers relating to - specific organisms - techniques (e.g. proteomics) - GO term names