Fwd: trying to get a foot in the door

[Kitsos Louis]

Oooops! Sorry everybody, last evening I answered Chris' email directly to him, rather than to the group. Here is is, then with his last answer. As mentioned in my reply to him, I'll have the googledoc ready sometime next week.

Ciao,

K.

Begin forwarded message:

From: Chris Mungall <cjmu...@lbl.gov>

Date: 02 Απριλίου 2013 7:59:53 μ.μ. GMT+0300

To: Kitsos Louis <lo...@imbb.forth.gr>

Subject: Re: trying to get a foot in the door

On Apr 2, 2013, at 9:32 AM, Kitsos Louis wrote:

Dear Chris,

I will answer in more detail in a few days (lots of other things to do: doctors, travel, etc.) and, my answer then may "degenerate" ;-) into a rather long google doc, especially as far as the relation between individual IDO extensions (in our case, VBDs) and the mother ontology are concerned. 

OK, great

Just a few words here, IDODEN is still in an alpha form and later this year we will release a beta with many of the items that you flagged (I'll answer those as well later) extensively edited. The reason we already made IDODEN available was in order to seek (with a "circular") feedback. corrections, etc., especially from the Dengue community.

Yes, I understand, often it makes sense to start with the specifics and generalize from there. I'm just worried that the generalization step won't happen and there will too much duplication of work, like there is with anatomy ontologies

Why in the Bioportal? Simply because many non-ontologologists, unfortutately, can't look at it using standard editing software.

Absolutely.

If you are interested, I could try and help you or your team set up an AmiGO instance, it's very configurable. This is the GO instance:

http://amigo2.berkeleybop.org/

You could add your own facets (e.g. mode of transmission). It does work best when there is annotation data underneath however.

There's other software you might find useful - e.g. you could set up an IDO TermGenie that allows curators to select external ontology terms (e.g. taxonomy) and apply a template to generate terms.This is a little harder configure but we aim to have this easier later this year.

Please be patient! 

K.

  

On Apr 2, 2013, at 6:57 PM, Chris Mungall wrote:

Hi Kitsos,

I'm curious about the IDO extensions approach and happened to pick on IDODEN to see examples of how it works.

I took a random example:

 / IDOMAL:0000000 ! process

  is_a GO:0008150 ! biological process

   is_a IDODEN_0000233 ! process of human host

    is_a IDODEN_0003571 ! physiological process of human host

     is_a IDODEN_0000235 ! cellular process of human host

      is_a IDOMAL:0000137 ! agglutination *** 

Why is "cellular process of human host" in a dengue-focused ontology, and "agglutination" and "process" brought in from a malaria-focused ontology?

Also, there are a few cases where you would benefit from equivalence axioms on the compositional classes:

 / IDOMAL:0000000 ! process

  is_a GO:0008150 ! biological process

   is_a GO:0051704 ! multi-organism process

    is_a IDODEN_0000228 ! dengue transmission -- part_of some 'occurence of dengue fever'

     is_a IDODEN_0000085 ! indirect dengue transmission process

      is_a IDODEN_0000086 ! vector borne dengue transmission process

       is_a IDODEN_0000087 ! mosquito borne dengue transmission process *** 

All classes like "mosquito borne dengue transmission process" should be composed from constituent classes like 'tranmission process', vector and pathogen. It can be tedious to do this manually but it saves work in the end, and there are tools like quickterm templates and the web based TermGenie tool we developed for GO to assist with exactly this kind of thing.

Sorry to pick on IDODEN, but this exemplifies a typical pattern I see, with a supposedly taxon-specific extension of IDO exhibiting a mix of expert biological knowledge that should actually be pushed up into a more general ontology so that it can be reused, and stuff that could either be scripted from a small kernel of species-specific knowledge, or brought in automatically from other sources (e.g. gene and protein databases).

As you say, there are particular patterns in IDODEN that are applicable to all VBDs. These might belong in a VBD extension of IDO. But it may be simpler to just add this to IDO itself rather than fussing with different ways to slice the cake.

A meeting would probably be a good idea but in the absence of a meeting I encourage you to write down your thoughts e.g. in a google doc or something and share with this group. This can be in any form but I like to encourage "design pattern" documents, analagous to design patterns in software engineering. Your thoughts on design patterns for VBDs would be particularly helpful. Some of these could later be translated into templates, e.g. for TermGenie.

On Apr 2, 2013, at 8:09 AM, Kitsos Louis wrote:

Hi Simon,

I'm not trying to "sell" IDODEN instead the FLU, but keep in mind that vector-borne diseases have the "inherent difficulty" of fitting vectors and all that go along in the ontology (three organisms instead of two!); and JE is a VBD! Believe me, it can't just be a "simple" extension of IDO.  I've proposed a meeting of IDO developers to try to sort out the different problems, but due to a variety of reasons this hasn't happened yet. 

Ciao,

K.

On Apr 2, 2013, at 3:05 PM, simon rayner wrote:

AG,

i am working on japanese encephalitis, so i was interested in the dengue extension.  However, influenza seemed a better place to start as it appears to be more established.  I also work on Bacillus cereus, so i look forward to the IDO-Staph notes

simon

On Tue, Apr 2, 2013 at 8:02 PM, simon rayner <simon.r...@gmail.com> wrote:

On Tue, Apr 2, 2013 at 6:23 PM, Albert Goldfain <albertg...@gmail.com> wrote:

Good timing with this question Simon! I am just now putting together a showcase of IDO-Staph applications and demos. The newest of these will be a case report form generator that generates CRFs linked to IDO-Staph.

Just curious, to what domain are you thinking of applying IDO to? 

Cheers,
AG

On Apr 2, 2013 4:38 AM, "Yu Lin" <lini...@gmail.com> wrote:

I think in Albert's paper: http://ceur-ws.org/Vol-897/session1-paper03.pdf

The NARSA Isolate Repository maybe is related data.

On Tue, Apr 2, 2013 at 4:34 AM, Kitsos Louis <lo...@imbb.forth.gr> wrote:

As far as I know, a rather early version of IDOMAL (an IDO extension) has been used for both the Malaria and the Dengue Decision Support Systems generated by the IVCC (@ Liverpool School of Tropical Medicine). I don't know, though, whether they've updated their DSSs to the updated IDOMAL and neither do I know whether the Dengue DSS has been updated to rely the early version of IDODEN that is already available.

K.

************************************************

Prof. Christos (Kitsos) Louis, MD, PhD

IMBB-FORTH (& Dept. Biol., U. Crete)

N. Plastira 100

700 13 Heraklion, Crete, Greece

************************************************

tel office:   +30-281 0391 119 and 

                 +30-281 0391 199 (after work)

tel mobile: +30-693 2735 566

fax:           +30-281 0391 104

************************************************

On 02 Απρ 2013, at 7:44 π.μ., SR wrote:

Dear all,

this might be a dumb post, but I've been trying to find examples where the IDO has been applied.  I can find posts about requests for new terms, papers about ontologies developed for specific pathogens and workshops about the IDO but nothing about application,  For example, I can download and open flu.owl and read it to see the terms, or make diagrams using protege, but who has adopted so i can try to play around and to make queries on some data?

thanking you in advance for your understanding...

Simon Rayner   

--
--
Google Groups "infectious-disease-ontology" group.
http://groups.google.com/group/ido-discuss
---
You received this message because you are subscribed to the Google Groups "infectious-disease-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ido-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
--
Google Groups "infectious-disease-ontology" group.
http://groups.google.com/group/ido-discuss
---
You received this message because you are subscribed to the Google Groups "infectious-disease-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ido-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
--
Google Groups "infectious-disease-ontology" group.
http://groups.google.com/group/ido-discuss
---
You received this message because you are subscribed to the Google Groups "infectious-disease-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ido-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
--
Google Groups "infectious-disease-ontology" group.
http://groups.google.com/group/ido-discuss
---
You received this message because you are subscribed to the Google Groups "infectious-disease-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ido-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
Simon Rayner

State Key Laboratory of Virology
Wuhan Institute of Virology
Chinese Academy of Sciences
Wuhan, Hubei 430071
P.R.China

+86 (27) 87199895 (office)
+86 18627113001 (cell)

--
Simon Rayner

State Key Laboratory of Virology
Wuhan Institute of Virology
Chinese Academy of Sciences
Wuhan, Hubei 430071
P.R.China

+86 (27) 87199895 (office)
+86 18627113001 (cell)

--
--
Google Groups "infectious-disease-ontology" group.
http://groups.google.com/group/ido-discuss
---
You received this message because you are subscribed to the Google Groups "infectious-disease-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ido-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

*******************************************

Prof. Christos (Kitsos) Louis
IMBB-FORTH & Dept. Biology, U. Crete
N. Plastira 100
700 13 Heraklion, Crete, Greece
*******************************************
tel office: +30 281 0391 119 and
+30 281 0391 199
tel mobile:  +30 693 2735 566
fax: +30 281 0391 104

--
--
Google Groups "infectious-disease-ontology" group.
http://groups.google.com/group/ido-discuss
---
You received this message because you are subscribed to the Google Groups "infectious-disease-ontology" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ido-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

*******************************************

Prof. Christos (Kitsos) Louis
IMBB-FORTH & Dept. Biology, U. Crete
N. Plastira 100
700 13 Heraklion, Crete, Greece
*******************************************
tel office: +30 281 0391 119 and
+30 281 0391 199
tel mobile:  +30 693 2735 566
fax: +30 281 0391 104

************************************************

Prof. Christos (Kitsos) Louis, MD, PhD

IMBB-FORTH (& Dept. Biol., U. Crete)

N. Plastira 100

700 13 Heraklion, Crete, Greece

************************************************

tel office:   +30-281 0391 119 and 

                 +30-281 0391 199 (after work)

tel mobile: +30-693 2735 566

fax:           +30-281 0391 104

************************************************