I'd like to extract, for a rather long list of human genes, info on tissues or cell types where they are known to be important in some automated way from literature. Any suggestions for where to start? Extracting Gene Ontology terms will miss many known gene-tissue associations. Is there a text mining tool that can find gene/cell-type associations?
I want to easily annotate, share and compare gene sets with other group members. What is the best tool? I have looked at Gene Set Builder, WebGestalt and Genephony. Have not found exactly what I'm looking for. What do you use?
I'm thinking about putting a proposal to bring our data resources kicking and screaming into the Semantic Web. I'm thinking RDF publishing, Linked Data compliance, microformats, ontological tagging. Has anyone been involved in a project like this? Anyone care to share experiences or ideas?
I'm looking for a semi-automatic way to associated genes with pathways/interaction data. Ideally, my scripts dump a gene list out, (either to file, or to an API), and the program shoots back relevant pathways (and maybe enrichment scores). Any suggestions?