Access typedefs from `Ontology` instance

[vlmir]

Access typedefs from `Ontology` instance

[puethe]

Thanks! That's very helpful and works for me.

Since the 'term' and 'typedef' stanzas are structurally very similar, at least in obo, I personally probably would have created a base class from which both the 'Term' class and a similar 'Typedef' class inherit. That would allow catching the remaining properties of the typedefs, such as comments, definitions etc.

None of this, however, is crucial for me now, and might also just be my personal use case. So just go ahead and make a release if you like. Thanks again!

[althonos]

Actually they are extracted from OBO files, and used to instantiate new relationships. They are not however accessible from the Ontology they were extracted from, which would be a nice feature.

[althonos]

As a test:

>>> import pronto
>>> mondo = pronto.Ontology('http://purl.obolibrary.org/obo/mondo.obo')
>>> mondo['MONDO:0000065'].relations
{Relationship('disease_arises_from_feature'): [<MONDO:0005015: diabetes mellitus (disease)>],
 Relationship('is_a'): [<MONDO:0005385 {source="DC:0000281"}: >,
                        <MONDO:0020573: genetic predisposition to disease>]}

(disease_arises_from_feature is typedefed in the mondo.obo file).

[vlmir]

Hi Martin, thanks for your response. Unfortunately, it doesn't address the problem I have, probably I was not clear enough about it. Let me re-state my question. As I understand it, correct me if I'm wrong, Pronto generates objects corresponding only to the [Term] stanzas but not to the [Typedef] stanzas. You see, my concern is Typedefs, not Relationships. Consequently, the exports from Pronto are completely devoid of [Typedef] stanzas. Moreover, the exported ontologies are effectively molded into taxonomies built exclusively on subsumption - there are 'is_a:' statements but no 'relationship:' statements. Thus, Pronto apparently fails to preserve the semantics present in the input ontologies. Have I missed something here? Is there any way to specify what should be included in the exports? Hope to hear from you soon, Vladimir P.S. I exported from Pronto like this: with open('test.obo', 'w') as fp: fp.write(onto.obo)

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On Tue, 10 Jul 2018 at 12:01, Martin Larralde ***@***.***> wrote: As a test: import pronto mondo = pronto.Ontology('http://purl.obolibrary.org/obo/mondo.obo')print(mondo['MONDO:0000065'].relations)```python {Relationship('disease_arises_from_feature'): [<MONDO:0005015: diabetes mellitus (disease)>], Relationship('is_a'): [<MONDO:0005385 {source="DC:0000281"}: >, <MONDO:0020573: genetic predisposition to disease>]} (disease_arises_from_feature is typedefed in the mondo.obo file). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#19 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA_SxLFKj7rX2wkAchm-wJoKs7iL2Sm6ks5uFHtggaJpZM4VHb6B> .

[althonos]

Hi Vladimir,
I was talking about this, but I didn't think about the exported OBO, and indeed it will contain no typedefs, which is a problem.

What I think I'll do is adding a typedefs attribute to Ontology instances, containing only the typedefs defined in the ontology file. I will then be able to serialized only the referenced typedefs when exporting.

I don't think this will be too complicated to do, so I'll try to work on it this week-end.

[vlmir]

Hi Martin, does this mean that Pronto, after all, parses Typedefs and retains them in the ontology objects? If so, then I'd like first to make clear that I have no vested interest in the OBO export, I used it just as a sanity check. I came across Pronto in a quest for a tool enabling Turtle/TTL serialization of ontologies. That's my primary interest. Turtle is gradually becoming a de facto standard language for Semantic Web implementation, ousting luckily the original RDFXML standard. My second interest is to have exports to JSON. Are Pronto objects serializable via the Python 'json' module? If not, would it be possible for you to implement a function transforming native objects into json serializable ones like they do in the NetworkX library? Hope to hear from you soon, Vladimir

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On Thu, 19 Jul 2018 at 13:52, Martin Larralde ***@***.***> wrote: Hi Vladimir, I was talking about this, but I didn't think about the exported OBO, and indeed it will contain no typedefs, which is a problem. What I think I'll do is adding a typedefs attribute to Ontology instances, containing only the typedefs defined in the ontology file. I will then be able to serialized only the referenced typedefs when exporting. I don't think this will be too complicated to do, so I'll try to work on it this week-end. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#19 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA_SxNmrQj2GYedJPNCldljc_MhXpOTBks5uIHMJgaJpZM4VHb6B> .

[althonos]

It parses them but do not hold them in ontology objects, only as Relationship instances.

The Turtle parser will probably take more time since I'm not familiar with the format or the available parser libraries.

Exporting ontologies to JSON is already possible, though, using the Ontology.json property ! 😉 Although it's more of a dump of the internal data representation, and does not follow a specific JSON ontology format (such as obojson).

[vlmir]

Hi Martin, what you say about json is already a good news. I personally don't care much about what they contemplate about json at the OBO Foundry. The most important thing for me is that I can get a json serialization fully representative of the Ontology object. Is the usage of the Ontology.json is anywhere documented? Cheers, Vladimir

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On Fri, 20 Jul 2018 at 15:47, Martin Larralde ***@***.***> wrote: It parses them but do not hold them in ontology objects, only as Relationship instances. The Turtle parser will probably take more time since I'm not familiar with the format or the available parser libraries. Exporting ontologies to JSON is already possible, though, using the Ontology.json property ! 😉 Although it's more of a dump of the internal data representation, and does not follow a specific JSON ontology format (such as *obojson*). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#19 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA_SxEX_dTl5JH83F74V8lXZuvtEaPaeks5uId94gaJpZM4VHb6B> .

[althonos]

It's listed on the Ontology reference (http://pronto.readthedocs.io/en/latest/pronto/pronto.Ontology.html#pronto.Ontology.json), but the documentation is not explanatory at all 😊

Basically the JSON should contain all terms referenced by accession, as well as metadata.

[vlmir]

Thanks, Martin, I'll have a look. Vladimir

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On Sat, 21 Jul 2018 at 21:51, Martin Larralde ***@***.***> wrote: It's listed on the Ontology reference ( http://pronto.readthedocs.io/en/latest/pronto/pronto.Ontology.html#pronto.Ontology.json), but the documentation is not explanatory at all 😊 Basically the JSON should contain all terms referenced by accession, as well as metadata. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#19 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA_SxEKo3H0xaOlissR_d5jIhGDUTqHdks5uI4ZQgaJpZM4VHb6B> .

[puethe]

Hi there,
I just stumbled over the same issue. Have you managed to have a look at it yet?
I'm using Pronto to import data from ontology files into a database and basically can't establish relationships between terms before adding the corresponding typedefs to the database.
If you don't have the time, I can also offer to have a look at it myself and open a pull request. Let me know.
Cheers,
Christoph

[althonos]

@puethe: I added a typedef attribute to Ontology instances, and added a obo property to the Relationship class so now exporting an ontology to obo format will export the [Typedef] stanzas, and you'll be able to access the typedefs declared in an ontology.

Could you test the master branch a bit to tell me if you need anything before I make a release ?

[althonos]

@puethe : I really wish I had more time to put into this library ! 😉

[althonos]

Fixed in release 0.11.0.