View source for HCLSIG BioRDF Subgroup/Tasks/Reagents/Status Reports/2006-04-17

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This note describes first attempts at translating the [http://www.alzforum.org/res/com/ant/default.asp Alzforum Antibody Directory] in to RDF.

'''Science Background''': http://en.wikipedia.org/wiki/Antibody

'''Goal of this round''': Review the contents of the database, start building a model (ontology), translate the database using it, see what problems arise.

'''Technology''': I am targeting OWL, using custom [http://svn.mumble.net/svn/lsw/ tools] written in a [http://armedbear.org/abcl.html java-based common lisp] which use the [http://www.mindswap.org/2003/pellet/ Pellet] libraries.

'''Selected Issues''':

* Namespace - what form of URI's to use for the various entities
** http://www.w3.org/2001/sw/hcls/ontologies/reagent.owl# for the ontology
** http://www.alzforum.org/res/com/ant# for the Alzforum specific fields
* Model - How to model the various entities
** The antibody isotype (e.g. IgG versus IgM), light versus heavy chain
** Experimental Methods that this antibody can be used for (http://www.alzforum.org/res/com/ant/glossary.asp) Note there are implicit relations between methods that should be modeled (e.g. more and less general terms)
** Sample Preparations - e.g. frozen sections, cells etc.
** Construction - how the antibody was created
** Epitopes - the part of the protein the antibody binds to
** Source - how the antibody was created, and in which species
** Reactivity/Specificity - what forms of the protein (e.g. phosphorylated) in which species (and which not)
* Connecting to existing ontologies, vocabularies - which to use
** Species: NCBI taxonomy?
** Gene: lsid? ncbi entrez URL?
** Methods: PSI-MI insufficient,  SNOMED? 
** Epitope: Sequence ontology? - but no way to specify e.g positional range of a sequence
** Company information - foaf? vcard?
* Parsing - Important information is in a restricted but varying subset of natural language
** Gene name is sometimes a standard name, sometimes not (e.g. embedded greek letter xml entities)
** Epitope descriptions (a variety of sorts of description)
** Reactivity/Specificity (mostly species, but with negative information, such as ''not'' mouse)
** Applicable experimental methods (some methods were not in glossary). May be list, may include negative information
** Method Glossary (manipulated in emacs to lisp form -> generate owl from it) 

'''Files'''
* antibody-db-dump-2006-04-16.txt.gz - Source spreadsheet from [[AlzForum]] (Thanks Colin!) **
* antibody1.owl.gz - Just the basics Annotation properties for some of the  source fields as literals. A bit of modelling. **
* parsed-epitopes.txt - An initial attempt to take apart the epitope descriptions **
* [[Media:HCLSIG_BioRDF_Subgroup$$Tasks$$Reagents$$Status_Reports$$2006-04-17$antibody.lisp]] - Very messy, but that's real life. Next version will be cleaner.
* * Note that these files are not available publicly for the moment, but are available on request from mailto:alanr-w@mumble.net

[[Category:Hclsig]] [[Category:HclsigTask]]