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[bioontology-support] Resource Index questions

Ray Fergerson ray.fergerson at
Mon Mar 14 10:32:11 PDT 2011



Trish dug up some much better documentation about creating a Resource
Access Tool (RAT). It is attached. I would ignore the previous document I
sent and use this one instead.




From: Ray Fergerson [mailto:ray.fergerson at] 
Sent: Friday, March 11, 2011 5:10 PM
To: 'Twigger, Simon'
Cc: 'support at'
Subject: RE: Resource Index questions




Sorry for the delay in getting back to you. I have been working with our
contractors who actually write the Resource Access Tools to get them to
produce some documentation. I have attached what we have at the moment.
Frankly, this documentation is terrible. It may give you enough pointers
to get you started though. The second page is (the beginnings of)
documentation about how to write a RAT. We clearly need to invest some
effort here to produce a few pages of real documentation.


Can you give me the link that you cannot access? It is possible that we
have something out there that is better than this that I don't know about.




From: Twigger, Simon [mailto:simont at] 
Sent: Friday, March 04, 2011 2:23 PM
To: ray.fergerson at
Subject: FW: Resource Index questions


Hi Ray,

I was emailing Nigam about the resource index and getting other data into
it - he pointed to you as the person with info on created Resource Access
Tools for other dbs - can you point me to the right place? :)

I found this page but the link to one tutorial is forbidden to me and the
whole page looks out of date with your current tools.



-----Original Message-----
From: Nigam Shah [mailto:nigam at]
Sent: Fri 3/4/2011 4:08 PM
To: Twigger, Simon
Subject: Re: Resource Index questions

Hi Simon,

See inline for responses ...

On Fri, Mar 4, 2011 at 1:26 PM, Twigger, Simon <simont at> wrote:

>  Hi Nigam,
> I think you showed data on this but do you have PubMed indexed in the
> resource index yet - I couldnt see it on the public site but perhaps its
> development? If you have the data I'd be interested to poke around to
> how the automated indexing worked on some publications for a specific
> journal that is interested in seeing how these type of technology can
> enhance their publications.
Yes, it's not up on the public site. It's on our research machines.
Depending on how badly you want it, we can think of ways to get you
I will also get a date from Ray on when it will be out in production (and
that will save everyone additional ad hoc coding).

> Did you just use abstract data - I suppose I could just run that through
> the annotator to see what comes back but having the REST api access to a
> repository of this data would be nice so I could test some concepts I
Yes, we only use title and abstract so you can test using the Annotator

> On a related note, can you do boolean searches on the RI? It seems like
> doing AND when I add more than one term in the web interface, is that
> correct?
We do have a UNION as well. See
for 'union' in the POST calls). The UI only does an AND via the GET calls.

> It would be really interesting to get Rat Genome Database information
> here - a good test case for the other Model organism databases and Im
> Jennie Larkin would be happy if you could include the main MOD that
> supports. Like other MODs, a lot of our data is curated annotations
> ontology terms to things (Genes, QTL, rat strains, etc), these would be
> great to include as they should be of good quality but wont need the
> annotator - what are your plans for that?
We can accept such "reported" annotations .. e.g. MeSH terms on PubMed
papers. If a human already assigned a term, we simply propagate it through
the closure step. No need for the annotator. If you write a Resource
Tool (i.e. a RAT for the Rat Genome Database ;-)) then there are methods
handle such reported annotations. We provide template resource access
for you to work off from. Ray Fergerson is the best person to ask.

> RGD does have text notes on gene reports, the Strain records can have a
> of narrative and the Pathway pages have a lot of text so they would
> the annotator to get more of the content out of them.
You can handle both the reported and the annotator-generated annotations
the same resource access tool ...  Our goal is to have database
write the resource access tool for their own db and contribute it back to
us. That way we can scale to hundreds of resources in the RI.

> Let me know what you think. :)
> Cheers!

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