Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Resource Index questions

Ray Fergerson ray.fergerson at stanford.edu
Fri Mar 11 17:09:48 PST 2011


Simon,

 

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.

 

Ray

 

From: Twigger, Simon [mailto:simont at mcw.edu] 
Sent: Friday, March 04, 2011 2:23 PM
To: ray.fergerson at stanford.edu
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whole page looks out of date with your current tools.

Cheers!

S.


-----Original Message-----
From: Nigam Shah [mailto:nigam at stanford.edu]
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 mcw.edu> 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
in
> development? If you have the data I'd be interested to poke around to
see
> 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
access.
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
have.
>
Yes, we only use title and abstract so you can test using the Annotator
API.

>
> On a related note, can you do boolean searches on the RI? It seems like
its
> doing AND when I add more than one term in the web interface, is that
> correct?
>
We do have a UNION as well. See
http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_
User_Guide
(search
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
into
> here - a good test case for the other Model organism databases and Im
sure
> Jennie Larkin would be happy if you could include the main MOD that
NHLBI
> supports. Like other MODs, a lot of our data is curated annotations
linking
> 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
Access
Tool (i.e. a RAT for the Rat Genome Database ;-)) then there are methods
to
handle such reported annotations. We provide template resource access
tools
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
lot
> of narrative and the Pathway pages have a lot of text so they would
require
> the annotator to get more of the content out of them.
>
You can handle both the reported and the annotator-generated annotations
in
the same resource access tool ...  Our goal is to have database
maintainers
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!
>
Regards,
Nigam.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20110311/3a1a9556/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Generalized Steps for adding a new RAT.DOCX
Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
Size: 17403 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20110311/3a1a9556/attachment.DOCX>


More information about the bioontology-support mailing list