HCLSIG BioRDF Subgroup/Tasks/Reagents
Task Build RDF resources that describes various kinds of experimental reagents, starting with antibodies.
- /Status Reports/2006-04-17 - First go at it.
- /Status Reports/2006-05-04 - HCLS teleconference report.
- Initial RDF that captures: Gene, the fact that this is an antibody, various kinds of pages about the antibody, such as vendor documentation, and any other properties that are explicitly captured in the source material. Work with source material from http://www.exactantigen.com/ and the the Altzforum Antibody Directory and from full text neuroscience papers (using textpresso).
- Work with the Ontology task force to identify appropriate ontologies and vocabularies to use in the RDF.
- Identify other kinds of reagents for which information might be gathered.
- Write queries against the RDF to answer questions of the sort posed on the Alzforum's Desperately Seeking Antibodies forum.
- See if the sources of the information would consider incorporating RDF directly onto their web pages.
- Be aware of other BioRDF projects and identify and enable cross project queries, e.g. Disease to antibody via gene.
Use case context Helping researchers identify tools with which to do experiments. Suggested by Tim Clark.
Problem statement for this use case
Antibodies are used as probes for presence of a protein (or a particular state of one). For example, a genomics technology, such as microarray, siRNA, or TaqMan might indicate that the level of mRNA is perturbed in a system. An antibody could be used to verify the the protein level is similarly perturbed. Antibodies are also commonly used as Biomarkers and Diagnostics.
- Representative kist of proteins of interest to researchers in Neurosciences (start with Alzforum list)
- Identify corpus of papers for text extraction.
- Sentences talking about antibodies for text extraction training.
- First pass RDF for the hits scraped from exactantigen.
- First pass RDF for content of Alzform antibody resource.
- First pass RDF for text content.
- OWL Ontology for describing the above RDF
- Integrated OWL/RDF for the resources
- SPARQL queries for some of the Desperately seeking questions.
- Notes about what kind of information one would need to formulate other of those questions.
- Alzforum's Antibody directory
- Desperately Seeking Antibodies
- Reagent vocabulary from 2DE Gel Electrophoresis ontology
- western blot term in PSI-MI
- SWAN Vocabulary
- Protocol Online: a good source for definitions of assay methods, etc. (thanks DonHatfield)
Some links from KarenSkinner:
- Neuromics Antibodies by Category
- The Immune Epitope Database and Analysis Resource (IEDB)
- Genomics Resources for Immunology Research
- Terminology from NCI Immunoprotein, Immunologic_Techniques, Immunohistochemistry, Immune_System
Task supports and dependencies
Tools and Services
Timeline for Task Completion
- Stage 1 (3 month goals)
- Stage 2 (6 months goals)