Re: [Obo-taxonomy] [Obo-discuss] Amphibian Taxonomic Ontology

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Peter E. Midford

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Jul 7, 2009, 12:17:45 PM7/7/09

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Sarah,
I've had a look over your proposed ATO and I've got a
couple of comments:

1. Most taxa seem to include an author, year citation in its name. I
think this is a good thing and I hope you can fill in the ones with
missing citations. We already do this for some taxa, particularly
those that are mentioned in our curated papers, but not fully
identified. I think this is something that will make its way into
TTO, even if only as a synonym.

2. Inclusion of ranks - another batch of duplicated rank terms. I
need to make revisions to my rank ontology, then maybe the
stakeholders can get together and agree on the list of ranks needed
and the mechanism. I like the way OBOEdit shows particular taxa as
has_rank children of their rank - however, I see you've implemented
this by defining has_rank as an ordinary relationship, rather than
using has_property and marking has_rank as a metadata relationship.
By doing this, you have, at least, made has_rank visible to
reasoners. I don't think Chris Mungall will be very happy with this
for other reasons.

3. Your root - this is a more serious problem - both Amphibia
(Linnaeus 1758) and rank are subclasses of taxonomy v3. Ranks and
taxa are different enough that it doesn't seem to me like they should
have a common parent. The other problem is whether a taxa is_a
taxonomy. At best, it might be an instance_of a taxonomy - that would
at least be consistent with the view that entities in a taxonomy
ontology represent taxon concepts. Of course, I'm partial to that
view, but other people might wonder what properties of a taxonomy an
individual frog inherits - if a particular frog is an instance_of Rana
palustris, then it is also an instance_of taxonomy v3. Making
Amphibia an instance_of taxonomy avoids this as the transitive
inference would not apply in this case.

Since the worst thing to happy to an ontology submission is to be
ignored, I hope this will start the conversation on this ontology and
the design choices you made.

Cheers,

Peter

On Jul 3, 2009, at 13:42, sbhdbe wrote:

> I missed the request for the link to the ontology for review...so
> here it is!
>
> http://ontology1.srv.mst.edu/sarah/amphibian_taxonomy.obo
>
> Sorry again about the delay!
> Thanks,
> Sarah
>
> Sarah Havens
> Curator, Amphibian Anatomy ontology
> www.amphibanat.org
> 110B Schrenk Hall
> Rolla, MO 65409
> (573)341-4069
> sbh...@mst.edu
>
>
>
> -----Original Message-----
> From: obo-discu...@lists.sourceforge.net [mailto:obo-discu...@lists.sourceforge.net
> ]
> Sent: Wed 6/24/2009 1:52 PM
> To: obo-d...@lists.sourceforge.net
> Subject: Obo-discuss Digest, Vol 37, Issue 21
>
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> Today's Topics:
>
> 1. Re: context ontology (David Osumi-Sutherland)
> 2. Amphibian Taxonomic Ontology (sbhdbe)
> 3. Re: Amphibian Taxonomic Ontology (Peter E. Midford)
> 4. Re: Human Phenotype Ontology and Inheritance/Clinical course
> (Judith Blake)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Jun 2009 17:00:27 +0100
> From: David Osumi-Sutherland <dj...@GEN.CAM.AC.UK>
> Subject: Re: [Obo-discuss] context ontology
> To: Barry Smith <phis...@buffalo.edu>, Peter Robinson
> <peter.r...@charite.de>
> Cc: obo-d...@lists.sourceforge.net
> Message-ID: <577905C4-DA33-41E6...@GEN.CAM.AC.UK>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> On 23 Jun 2009, at 10:10, Barry Smith wrote:
>
>> Can you work on finding a better name for this? Even 'Genetic
>> Context Ontology' would be a step in the right direction.
>
> Agreed. Peter, if you're working on a new version, can you give it
> this name? We can then leave the old context ontology in place until
> we've made an effort to track down users to inform them of the name
> change.
>
>>
>> BS
>>
>
> David Osumi-Sutherland, PhD
> Ontologist / Curator
> Virtual Fly Brain / FlyBase
> Department of Genetics
> University of Cambridge
> Downing Street
> Cambridge, CB2 3EH
> UK
> +44 (0)1223 333 963
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 23 Jun 2009 14:14:27 -0500
> From: "sbhdbe" <sbh...@mst.edu>
> Subject: [Obo-discuss] Amphibian Taxonomic Ontology
> To: <obo-d...@lists.sourceforge.net>
> Message-ID:
> <7468EE0453D3224DB5F...@MST-VMAIL2.srv.mst.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
> We have been working on building an Amphibian Taxonomic Ontology
> that will allow for annotations with the Amphibian Anatomy
> Ontology. It includes all amphibian species and will be updated
> regularly to incorporate changes in taxonomgy. We are hoping to
> have it accepted by the OBO foundry and able to be on sourceforge.
> We are also hoping that it can be ATO if accepted.
> Thanks
> Sarah
>
> Sarah Havens
> Curator, Amphibian Anatomy ontology
> www.amphibanat.org
> 110B Schrenk Hall
> Rolla, MO 65409
> (573)341-4069
> sbh...@mst.edu
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 23 Jun 2009 14:30:58 -0500
> From: "Peter E. Midford" <petere...@yahoo.com>
> Subject: Re: [Obo-discuss] Amphibian Taxonomic Ontology
> To: obo-d...@lists.sourceforge.net
> Message-ID: <C8136DCE-3684-44CD...@yahoo.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Sarah,
> Where can we review this ontology?
>
> Peter
>
> On Jun 23, 2009, at 14:14, sbhdbe wrote:
>
>> Hi,
>> We have been working on building an Amphibian Taxonomic Ontology
>> that will allow for annotations with the Amphibian Anatomy
>> Ontology. It includes all amphibian species and will be updated
>> regularly to incorporate changes in taxonomgy. We are hoping to
>> have it accepted by the OBO foundry and able to be on sourceforge.
>> We are also hoping that it can be ATO if accepted.
>> Thanks
>> Sarah
>>
>> Sarah Havens
>> Curator, Amphibian Anatomy ontology
>> www.amphibanat.org
>> 110B Schrenk Hall
>> Rolla, MO 65409
>> (573)341-4069
>> sbh...@mst.edu
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Obo-discuss mailing list
>> Obo-d...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>
> --
> Peter Midford
> Phenoscape Ontology Curator
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 Jun 2009 13:09:46 -0400
> From: Judith Blake <Judith...@jax.org>
> Subject: Re: [Obo-discuss] Human Phenotype Ontology and
> Inheritance/Clinical course
> To: "obo-d...@lists.sourceforge.net"
> <obo-d...@lists.sourceforge.net>
> Cc: "mhae...@uoneuro.uoregon.edu" <mhae...@uoneuro.uoregon.edu>
> Message-ID: <C666849A.7B64%judith...@jax.org>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Really in this case I'm representing the very large phenotype group
> headed up by Janan Eppig. We encode much of this information in
> curation of mouse mutations and their modes of inheritance.
>
> Judy
>
>
> On 6/23/09 11:39 AM, "Suzanna Lewis" <su...@fruitfly.org> wrote:
>
> I'm there as well, but I think a phone call with David and Melissa is
> still needed. Judy and I aren't the ideal folk for this.
>
> -S
>
> On Jun 23, 2009, at 6:19 AM, Judith Blake wrote:
>
>> Peter,
>> I'll be at ISMB next week...and at BIoOntologies meeting. We can
>> chat then...see who else is there.
>>
>> Judy
>>
>> -----Original Message-----
>> From: Peter Robinson [mailto:peter.r...@charite.de]
>> Sent: Tuesday, June 23, 2009 8:52 AM
>> To: mhae...@uoneuro.uoregon.edu; obo-d...@lists.sourceforge.net
>> Subject: Re: [Obo-discuss] Human Phenotype Ontology and Inheritance/
>> Clinical course
>>
>> Melissa Haendel wrote:
>>> Hi all,
>>>
>>> ZFIN doesn't use the context ontology, except as a reference for
>>> how we
>>> record genotypes. We do not use the ontology identifiers etc.
>>>
>>> That said, I do think think that these two ontologies should either
>>> be
>>> merged, or should be brought into synchronization with xrefs and
>>> common
>>> definitions if they cannot be merged.
>>>
>>> We could certainly help with definitions, and I agree with David, I
>>> don't think this should be a terribly time consuming or
>>> controversial
>>> project.
>>>
>>> All MODs have to deal with genetic context in some manner, it would
>>> be
>>> good to have different perspectives. I think a new list and/or
>>> tracker
>>> would be a good start. It really would be fantastic if we had a
>>> full-fledged context ontology that was shared across different
>>> domains.
>>
>>
>>
>>
>>
>> If any of you will be at the ISMB, we could plan to meet about this
>> over
>> coffee. I will be at the Bio-Ontology SIG and in the main conference
>> on
>> Monday and Tuesday.
>> Otherwise I will plan on looking over both ontologies and would
>> make a
>> suggestion for what terms refer to the same thing and whether it
>> would
>> be sensible to merge or use xrefs, and we could plan a phone or email
>> conversation to work things out.
>>
>> cheers Peter
>>
>>
>>
>>
>>
>>
>>
>>
>>>
>>> Cheers,
>>> melissa
>>>
>>> David Osumi-Sutherland wrote:
>>>> Hi Peter,
>>>>
>>>> On 21 Jun 2009, at 12:07, Peter Robinson wrote:
>>>>
>>>>
>>>>> David Osumi-Sutherland wrote:
>>>>>
>>>>>> Hi Peter,
>>>>>>
>>>>>> I don't have much time to work on this right now, but given the
>>>>>> commonalities in much of genetics, I think it makes sense to keep
>>>>>> terms
>>>>>> like this in one common ontology. Can you just add your terms to
>>>>>> context.obo?
>>>>>>
>>>>>> I think the zebrafish people already use some terms from this,
>>>>>> and I
>>>>>> suspect they have some terms they can add. We should also
>>>>>> investigate
>>>>>> what MGI are using and perhaps bring in phenoscape. It makes
>>>>>> sense
>>>>>> to me
>>>>>> to start a small mailing list of interested parties.
>>>>>>
>>>>>> The size of the ontology and, i suspect, the issues involved are
>>>>>> much
>>>>>> less daunting than for the cell ontology so I think a communal
>>>>>> effort
>>>>>> should be able to work relatively quickly. As you have a clear
>>>>>> idea of
>>>>>> what you need, I think it'd be fine to just add the terms you
>>>>>> want
>>>>>> without discussion. If you need to change existing terms, I'd
>>>>>> make a
>>>>>> proposal and set some time limit (say two months?) for interested
>>>>>> parties to comment/object. Taking this approach, we'll have a
>>>>>> useful
>>>>>> shared ontology that can be gradually improved by communal
>>>>>> input as
>>>>>> time permits.
>>>>>>
>>>>>> Does this sound reasonable?
>>>>>>
>>>>>> David
>>>>>>
>>>>>>
>>>>> Hi David,
>>>>> I do have some doubts, because the ontology context.obo seems to
>>>>> lack
>>>>> focus. For instance, it mixes clinical terms such as "dominant"
>>>>> and
>>>>> "recessive" with cellular terms such as "cell autonomy of
>>>>> action". In
>>>>> any case it is not adequate to describe the modes of inheritance
>>>>> that
>>>>> are needed for the diseases being annotated by the HPO.
>>>>>
>>>>>
>>>> I think you're probably right that this should be two ontologies.
>>>> Splitting might not be totally straightforward though. One could
>>>> think
>>>> of 'maternal effect' (the phenotype is expressed only in the
>>>> offspring
>>>> of mutant mothers) as a 'mode of inheritance' or as describing the
>>>> relationship between mutant material and the location of
>>>> expression of
>>>> the phenotype. This is what 'autonomy of action' refers to - 'cell
>>>> non-autonomous' is used to describe cases where the phenotype is
>>>> expressed in wild-type cells in animals that are a mosaic of mutant
>>>> and wild-type cells.
>>>>
>>>>
>>>>
>>>>> I should think it would be good to get all interested parties
>>>>> talking
>>>>> about what sort of things need to be described and then decide if
>>>>> we
>>>>> can
>>>>> do this with a single ontology or whether it might be best to have
>>>>> two.
>>>>>
>>>> Agreed.
>>>>
>>>>> In any case, I need an ontology to describe modes of inheritance
>>>>> seen in
>>>>> human disease, basically as described here
>>>>> http://ghr.nlm.nih.gov/handbook/inheritance/inheritancepatterns
>>>>> but with some additional detail.
>>>>>
>>>>>
>>>> It seems to me it would be easy to add autosome-linked and sex-
>>>> chromosome-linked variants of recessive, dominant etc. Ditto
>>>> mitochondrial inheritance.
>>>>
>>>> Perhaps more challenging would be to devise definitions that cope
>>>> with
>>>> the way the terms recessive and dominant are used by evolutionary
>>>> biologists as well as by model organism and human medical
>>>> geneticists.
>>>>
>>>> Cheers,
>>>> David
>>>>
>>>>> cheers Peter
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On 21 Jun 2009, at 08:41, Peter Robinson wrote:
>>>>>>
>>>>>>
>>>>>>>>> Hi Suzi,
>>>>>>>>> actually, the phenotypic manifestation ontology in the link is
>>>>>>>>> much
>>>>>>>>> less
>>>>>>>>> complete than what we already have (there are 29 terms), and
>>>>>>>>> doesnt
>>>>>>>>> contain
>>>>>>>>> the information required to describe modes of inheritance in
>>>>>>>>> human
>>>>>>>>> genetic
>>>>>>>>> disease.
>>>>>>>>>
>>>>>>>> Okay, would you be willing to absorb these 29 terms into what
>>>>>>>> you
>>>>>>>> have
>>>>>>>> so that we get the benefits, but without losing anything. My
>>>>>>>> main
>>>>>>>> concern is that we get convergence and a single source for this
>>>>>>>> type
>>>>>>>> of information. Then we can replace that ancient one with what
>>>>>>>> you have.
>>>>>>>>
>>>>>>>>
>>>>>>> OK. The HPO will plan on splitting off the inheritance/clinical
>>>>>>> course
>>>>>>> subontologies into separate ontologies during the course of
>>>>>>> July.
>>>>>>> I will
>>>>>>> take a look at the terms above, some of which are already
>>>>>>> represented in
>>>>>>> HPO.
>>>>>>> -Peter
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Dr. med. Peter N. Robinson, MSc.
>>>>>>> Institut f?r Medizinische Genetik
>>>>>>> Universit?tsklinikum Charite
>>>>>>> Humboldt-Universit?t
>>>>>>> Augustenburger Platz 1
>>>>>>> 13353 Berlin
>>>>>>> Germany
>>>>>>> voice: 49-30-450569124
>>>>>>> fax: 49-30-450569915
>>>>>>> email: peter.r...@charite.de
>>>>>>> http://compbio.charite.de/
>>>>>>> http://www.human-phenotype-ontology.org
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>>
>>>>>>> Are you an open source citizen? Join us for the Open Source
>>>>>>> Bridge
>>>>>>> conference!
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>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Obo-discuss mailing list
>>>>>>> Obo-d...@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>>>>>
>>>>>> David Osumi-Sutherland, PhD
>>>>>> Ontologist / Curator
>>>>>> Virtual Fly Brain / FlyBase
>>>>>> Department of Genetics
>>>>>> University of Cambridge
>>>>>> Downing Street
>>>>>> Cambridge, CB2 3EH
>>>>>> UK
>>>>>> +44 (0)1223 333 963
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>>> Dr. med. Peter N. Robinson, MSc.
>>>>> Institut f?r Medizinische Genetik
>>>>> Universit?tsklinikum Charite
>>>>> Humboldt-Universit?t
>>>>> Augustenburger Platz 1
>>>>> 13353 Berlin
>>>>> Germany
>>>>> voice: 49-30-450569124
>>>>> fax: 49-30-450569915
>>>>> email: peter.r...@charite.de
>>>>> http://compbio.charite.de/
>>>>> http://www.human-phenotype-ontology.org
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Are you an open source citizen? Join us for the Open Source Bridge
>>>>> conference!
>>>>> Portland, OR, June 17-19. Two days of sessions, one day of
>>>>> unconference: $250.
>>>>> Need another reason to go? 24-hour hacker lounge. Register today!
>>>>> http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org
>>>>> _______________________________________________
>>>>> Obo-discuss mailing list
>>>>> Obo-d...@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>>>
>>>> David Osumi-Sutherland, PhD
>>>> Ontologist / Curator
>>>> Virtual Fly Brain / FlyBase
>>>> Department of Genetics
>>>> University of Cambridge
>>>> Downing Street
>>>> Cambridge, CB2 3EH
>>>> UK
>>>> +44 (0)1223 333 963
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Are you an open source citizen? Join us for the Open Source Bridge
>>>> conference!
>>>> Portland, OR, June 17-19. Two days of sessions, one day of
>>>> unconference: $250.
>>>> Need another reason to go? 24-hour hacker lounge. Register today!
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>>>> _______________________________________________
>>>> Obo-discuss mailing list
>>>> Obo-d...@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>>
>>>
>>
>>
>> --
>> Dr. med. Peter N. Robinson, MSc.
>> Institut f?r Medizinische Genetik
>> Universit?tsklinikum Charite
>> Humboldt-Universit?t
>> Augustenburger Platz 1
>> 13353 Berlin
>> Germany
>> voice: 49-30-450569124
>> fax: 49-30-450569915
>> email: peter.r...@charite.de
>> http://compbio.charite.de/
>> http://www.human-phenotype-ontology.org
>>
>> ------------------------------------------------------------------------------
>> Are you an open source citizen? Join us for the Open Source Bridge
>> conference!
>> Portland, OR, June 17-19. Two days of sessions, one day of
>> unconference: $250.
>> Need another reason to go? 24-hour hacker lounge. Register today!
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>> _______________________________________________
>> Obo-discuss mailing list
>> Obo-d...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>
>> ------------------------------------------------------------------------------
>> Are you an open source citizen? Join us for the Open Source Bridge
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>> _______________________________________________
>> Obo-discuss mailing list
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>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>
>
>
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--
Peter Midford
Mesquite Developer

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