[MOBY-dev] Progress on services and object question

[Simon Twigger]

Hi there,

I managed to get my prototype pubmed service functioning this evening when
I get things a little more functional I'll try and register all the right
things at the main MOBY central so others can give it a try.

Right now, it takes a keyword and runs a search on PubMed, returning
PubMed Ids for matching records. In due course a second service will then
take a PubMedID and return the full record.

Passing a single keyword is a crazy way to search PubMed - youd never want
to do anything like that, particularly for this particular application -
running regular screens of PubMed for articles relevant to your model
organism. Ideally you'd search with keyword(s) combined with date and
perhaps author.  However, given that one can only pass a single thing into
a MOBY service, Im wondering how to cleanly overload that one thing - eg.
keyword and date, keyword, author and date. My thought would be to define
an object as a pubmed entrez query string, eg. things like "rat[TIAB] AND
2003[DP]" to search for rat in title and author and limit to 2003.

Thinking out loud - can I pass in a complex object as opposed to a string
from a particular namespace (the assumption being that the string is a
single thing -accession, keyword, go ID, etc)? Presumably I could define a
literature search object with an xsd, etc. and use that  as the input
object containing elements for keywords, dates, etc.? This would probably
be a cleaner solution and would save other people worrying about arcane
entrez query creation. Is this the correct way to be thinking about this?

Cheers,

    Simon.