Cryo Electron Microscopy Ontology

[sanlopez]

Use this form to register a new ontology with the OBO Foundry. Please read the instructions provided here: http://obofoundry.org/docs/NewOntologyRegistrationInstructions.html

Ontology title

Cryo Electron Microscopy Ontology

Requested ID space

cryoem

Ontology location

https://github.com/I2PC/cryoem

Contact person

Name: Carlos Oscar Sorzano Email address: coss@cnb.csic.es GitHub username: cossorzano

Issue tracker

https://github.com/I2PC/cryoem/issues

Ontology license

• [ ] CC0 (public domain)
• [X] CC-BY (version 3 or later)
• [ ] Other: please specify

Available ontology formats

OWL-RDF/XML and OBO

What domain is the ontology intended to cover?

Imaging

Related OBO Foundry ontologies

chmo, ero, fix and omit.

Intended use/related projects

This ontology describes data types and image processing operations in Cryo Electron Microscopy of Single Particles. The objects and protocols labeled in this ontology are the ones used in the cryo em image processing framework Scipion.

Data source

Scipion framework (http://scipion.i2pc.es/)

[bpeters42]

Thank you for the submission. Cryo EM is very much in the scope of OBI. It would be fantastic if you could contribute your effort into that broader ontology, which will also give your work much higher visibility.

[bpeters42]

To add to that: the OBI team would be happy and excited to make that happen, we have existing mechanisms to allow experts in specific experimental areas to flesh out sets of terms relevant to them, and integrate them with the broader OBI framework. Happy to explain more on this tracker or by email or (ideally) if you join one of the OBI calls.

[sanlopez]

Thank you for your proposal, we would be pleased to enrich OBI with the terms that may be interesting for you. However, after checking the OBI entities, we are not sure if all the terms of our ontology suits any of them. Therefore could it be possible to enriched OBI with some terms (the ones that are relevant to you) and also to have the ID space we have requested to the OBO Foundry?

[matentzn]

@sanlopez Thank you for checking in! Could you provide us with a list of terms you are worried that could be out of scope? One of the most important jobs of the OBO foundry is to try and avoid overlapping scope in ontologies, as this makes term re-use increasingly difficult. We are very open to helping you get all your terms in their correct ontology so that other people can easily make use of them as well. Unless of course, your concern is not where the terms go, but something else? If so, let us know as well!

[sanlopez]

@matentzn thanks again for your help. In general terms, in which OBI entity/category do you think the cryo em objects and protocols described this ontology could fit in?

[bpeters42]

Irene: That is not how it works. YOU are asking to include your ontology on Cryo-EM into OBO. Cryo-EM is an experimental technique. There is an ontology for experimental techniques in OBO, which is OBI. And OBI was created specifically for the purpose of making descriptions of experiments with different techniques interoperable.

If you think Cryo-EM is special and needs different handling from what OBI does, you can 1) Make an argument to point out what part of Cryo-EM experiments cannot be represented in OBI. but it is YOUR job to tell us. You can't ask Nico to do this work for you. 2) Create your own ontology outside of OBO to address your user needs. Nothing wrong with that, and from your responses, I would recommend you do that.

• Bjoern

On Sat, Feb 13, 2021 at 8:01 AM Irene notifications@github.com wrote:

@matentzn https://github.com/matentzn thanks again for your help. In general terms, in which OBI entity/category do you think the cryo em objects and protocols described this ontology could fit in?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1426#issuecomment-778637910, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IXG7CE4M3SBWZIGPALS62O5DANCNFSM4XJUALBQ .

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[cossorzano]

Dear Bjoern and Maten,

thank you both for having a look at this issue and explaining us better the goals of OBO OBI. What we are afraid of is that our few classes get lost in a huge ontology with about 4,000 entities among classes as varied as 2x2 factorial design (a statistical concept), B-cell (immunology), and nasal cavity (anatomy), and none of them related to the modeling we need in our domain. We do not find many of the concepts related to Electron Microscopy Single Particle Analysis, although there is one "electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex" that seems to be a too specific experiment of Single Particle Analysis or Electron Tomography.

In any case, thanks a lot for your help, and we will look for some better place for the ontology.

[matentzn]

Hey @cossorzano

The way we typically go about this is this:

1. We get our terms into the most suitable ontology, lets say for the sake of this explanation, these are OBI, STATO and Uberon.
2. You then create something called an "application ontology". This term is a bit contested, but the idea is this: you provide a set of terms as an input, and as an output, you get an ontology containing only the terms you are interested in. There are a few such examples, I can dig out more, such as https://github.com/EBISPOT/scatlas_ontology. Note that application ontologies (or, to avoid terminological confusion: "ontologies tailored for a particular application") are not added to OBO, but usually follow OBO principles. Application ontologies import terms from other ontologies.

By doing this, 1) you have a significant impact on open science - large widely use ontologies such as OBI and Uberon are improved by your input, which makes the world better for everyone. 2) you get an ontology that is tailored just for your specific use case as well (the above example, for example, is used to index the single cell atlas search engine, but there are other examples that are used in curation interfaces, such as EFO and others).

Happy to advice further on this process!

[jamesaoverton]

Since I was already writing my reply, let me agree with @matentzn with slightly different emphasis.

OBI is just one example of the OBO commitment to bringing together diverse communities of people so that we can integrate diverse sets of data. Nobody uses all of OBO for a single project, and likewise nobody uses all of OBI for a single project. For example, immunologists working on a given study use one set of OBI terms to describe their experiments, while toxicologists working on another study use a different set of terms. As @matentzn says, we have tools for extracting just the terms you need. But the immunologists and the toxicologists are both using terms for study designs, devices, assays, data processing, etc. By agreeing on these broader terms and patterns, they make it possible to integrate their data. I find it surprising how many fields overlap in interesting ways, and how hard it is to say in advance which ontology terms a given project will need.

It's hard to make a good ontology for one group to use. It's much harder to make an ontology for many groups to use, but the benefits for data integration are much greater.

[balhoff]

We'll go ahead and close the request per discussion in OBO operations meeting 2021-03-09.

[matentzn]

@cossorzano @sanlopez Please feel free to reach out if you have questions or would like to discuss this further! Very happy to answer any questions and help out anywhere I can :)

[matentzn]

BTW this request was closed because you seem to have changed your mind "In any case, thanks a lot for your help, and we will look for some better place for the ontology." - If it's about getting a PURL, I can also recommend https://github.com/perma-id/w3id.org which we have used in many other projects.

[sanlopez]

@matentzn thanks a lot for you help. And sorry about the inconvenience this may have caused, we are kind of newbies in the ontology ecosystem.

[matentzn]

@sanlopez feel also free to join our slack space! I sent you an email (to your gmail) with an invite!