DNA and RNA as sequence attributes vs. chemicals

[paolaroncaglia]

Hi,

EFO would like to import the SO terms for ‘DNA’ and ‘RNA’ (SO:0000352 and SO:0000356 respectively), but these currently do not align with ChEBI’s definition of DNA and RNA molecule:

In ChEBI, deoxyribonucleic acid is_a nucleic acid, which is a descendant of chemical entity,

But in SO, DNA is_a nucleic acid, which is_a polymer_attribute, which is_a sequence_attribute.

We are debating on whether EFO should see DNA and RNA as chemicals, or as physical regions. Depending on the resolution, EFO will need to add a new branch for DNA and RNA molecules and axiomatise them to terms from one of the two ontologies. Could you please comment on the SO view of DNA and RNA as related to sequences rather than chemicals?

Thanks, Paola

[keilbeck]

Hi Paola We are working on a newer version of SO where the molecular entities are integrated with the top level of Chebi, and the corresponding sequence features are dependent continuants of some form. @mikebada is the person you should talk to.

In my opinion, where you integrate these terms depends on what your intent is. Are you modelling the information carrying potential or the molecular/physical properties?

--K

[paolaroncaglia]

Hi @keilbeck and @mikebada,

Thanks - great to hear that you guys are working towards integration with ChEBI. May I please ask if there are any plans in terms of timeframe to achieve that? The modelling issue is tricky for us too (DNA vs RNA = chemical, RNA vs ncRNA = information-carrying potential, ncRNA vs snRNA = location etc.) and it sounds like EFO may wish to mirror your future classification. I’m discussing with my colleagues. Thanks,

Paola

[mellybelly]

Hi @paolaroncaglia would be great to discuss as we would like to define requirements for a molecular phenotype ontology, and how these phenotypes relate to GO, GENO, and SO will be important. @cmungall @mbrush

[paolaroncaglia]

Hi @mellybelly , I’ll leave that discussion to @cmungall as I’m no longer with GO :-} Thanks!

[mikebada]

Hi Paola,

Our plan is for an ontology named the MSO (Molecular Sequence Ontology) composed of analogs of the large majority of current SO classes; this ontology is a representation of material entities (as well as their specific dependent continuants and some associated occurrents), and these are the sequence entity classes that are integrated within ChEBI. The SO then remains as an ontology of sequence entities represented as generic dependent continuants (GDCs) (as has been reported, though many/most of the actual definitions don’t actually seem to represent GDCs), and the SO GDC classes and can then be defined necessarily and sufficiently in terms of their corresponding MSO classes.

I think we have a pretty good draft version of the MSO ready, but I’ll let Karen respond with her thoughts on a timetable.

Lemme know if you have any more questions...

Cheers, Mike

From: paolaroncaglia notifications@github.com<mailto:notifications@github.com> Reply-To: The-Sequence-Ontology/SO-Ontologies reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, June 7, 2017 at 2:39 AM To: The-Sequence-Ontology/SO-Ontologies SO-Ontologies@noreply.github.com<mailto:SO-Ontologies@noreply.github.com> Cc: Mike Bada mike.bada@ucdenver.edu<mailto:mike.bada@ucdenver.edu>, Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [The-Sequence-Ontology/SO-Ontologies] DNA and RNA as sequence attributes vs. chemicals (#400)

Hi @keilbeckhttps://github.com/keilbeck and @mikebadahttps://github.com/mikebada,

Thanks - great to hear that you guys are working towards integration with ChEBI. May I please ask if there are any plans in terms of timeframe to achieve that? The modelling issue is tricky for us too (DNA vs RNA = chemical, RNA vs ncRNA = information-carrying potential, ncRNA vs snRNA = location etc.) and it sounds like EFO may wish to mirror your future classification. I’m discussing with my colleagues. Thanks,

Paola

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/The-Sequence-Ontology/SO-Ontologies/issues/400#issuecomment-306729515, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHEa3QzzsYZYiaRe9fYRwCfsf--2q5mJks5sBmHHgaJpZM4Nrlq0.

[paolaroncaglia]

Hi @mikebada and @keilbeck ,

Thanks! We'd love to use MSO, it would fit EFO users very nicely. Would it be possible to use an MSO first version already? If not, please let us know your thoughts in terms of timeframe - so we can assess what the best avenue is for us - it wouldn't be sensible to duplicate efforts on this, but it'd be great to fix those terms in EFO sooner rather than later :-)

Best wishes, Paola

[keilbeck]

We should have a version of it on github this week. It would be great if you were a user.

[mikebada]

Hi Paola,

We’ve put our draft MSO.owl on the SO GitHub site for you to take a look at. We recommend you use FaCT++ (which is included in Protege 5) to classify the ontology.

A quick overview: The MSO classes are integrated within high-level classes of the BFO and ChEBI ontologies. The analogs of the large majority of the SO classes (and the ones you’re most likely interested in) are under CHEBI:’chemical entity’, and more specifically, CHEBI:’molecular entity’ and CHEBI:group. Beneath the former, we’ve created a new fundamental class called sequence molecular entities, which encompass all ChEBI molecular entities that have sequences: nucleic acids, nucleic acid strands, and peptides. Beneath the latter are sequence molecular entity regions, which are segments of one or more residues as parts of sequence molecular entities. Sequence junctions and termini are for now placed under BFO:’immaterial entity’, and sequence attributes that we’ve kept are under BFO:’specifically dependent continuant’, and more specifically distributed between BFO:quality and BFO:disposition.

Hopefully this will help get you started. Let us know if you have any questions...

Cheers, Mike

From: paolaroncaglia notifications@github.com<mailto:notifications@github.com> Reply-To: The-Sequence-Ontology/SO-Ontologies reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, June 14, 2017 at 4:29 AM To: The-Sequence-Ontology/SO-Ontologies SO-Ontologies@noreply.github.com<mailto:SO-Ontologies@noreply.github.com> Cc: Mike Bada mike.bada@ucdenver.edu<mailto:mike.bada@ucdenver.edu>, Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [The-Sequence-Ontology/SO-Ontologies] DNA and RNA as sequence attributes vs. chemicals (#400)

Hi @mikebadahttps://github.com/mikebada and @keilbeckhttps://github.com/keilbeck ,

Thanks! We'd love to use MSO, it would fit EFO users very nicely. Would it be possible to use an MSO first version already? If not, please let us know your thoughts in terms of timeframe - so we can assess what the best avenue is for us - it wouldn't be sensible to duplicate efforts on this, but it'd be great to fix those terms in EFO sooner rather than later :-)

Best wishes, Paola

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/The-Sequence-Ontology/SO-Ontologies/issues/400#issuecomment-308391302, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHEa3QDyFk1e60mLuQd5O8ce62flNMtUks5sD7YcgaJpZM4Nrlq0.

[paolaroncaglia]

@mikebada and @keilbeck many thanks for making the MSO file available! I'll take a look and will discuss with my colleagues at EFO hopefully by the end of this week (sorry for the delay, we've all been a bit busy). Cheers, Paola

[keilbeck]

Paola - I am working through it to. The IDs are a bit rough and I am compiling a list of questions/comments for Mike. One of the things to be aware is that the ontology contains both MSO and SO ids but they are all really MSO terms, in the final version, there would just be MSO IDS, and SO will be automatically generated.

[paolaroncaglia]

Hi @keilbeck and @mikebada , Sorry for the delay. Due to paper resubmissions, conferences etc, I’ve just started looking at MSO, while my colleagues at EFO haven’t had a chance yet. At first glance, it looks like EFO could successfully import MSO terms for DNA and RNA branches. Since @keilbeck noted that she was going through the MSO draft in her latest comment, I was wondering if there’s any update that I should be aware of before I discuss MSO integration with my colleagues. Thanks!

[cmungall]

Should comments on MSO be posted on this tracker? Will the source for it be maintained in this repo?

My main question is about updates - how will SO and MSO be kept in sync?

[paolaroncaglia]

Hi @keilbeck, @mikebada and @cmungall, Based on previous comments from @keilbeck and @cmungall, I’m not sure if MSO is stable enough already to be imported into other ontologies such as EFO. I’ll wait to hear from you if there’s any update on those previous comments. Thanks and happy summer to everyone!