NTR: metabolomics terms

[nicolevasilevsky]

JP has a list of metabolomics term requests for HPO, see the spreadsheet here.

These look pretty straightforward, I can start working on adding these.

cc @pnrobinson

[drseb]

It would be better not to "only" add to HPO, but let HPO and HPOA go hand in hand here. I.e. for each new term, add the mentioned HPOA from the spreadsheet.

[pnrobinson]

I completely agree with Seb, please also add to HPOA!! As an aside, here is a new tool for doing HPO biocuration that might be helpful https://github.com/TheJacksonLaboratory/HPOworkbench

[nicolevasilevsky]

Sounds good!

[nicolevasilevsky]

@pnrobinson and @drseb - to add the annotations, I should use the HPO Phenote tool that you showed me, Peter?

But if I just added a new term to the HPO, will it take a bit before it is available in the HPO Phenote?

[pnrobinson]

Hi Nicole, if you add a term, it will not be available via the automatic download until the next HPO release. However, you can create a local version of the HPO and import it, and then you will see the new terms http://hpo-workbench.readthedocs.io/en/latest/latest.html @drseb I think we need to increase the pace of releases because we are doing lots of biocuration and will need to add the new terms to HPOA. Or is there another way?

[nicolevasilevsky]

@drseb would you mind MIREOTing these Chebi terms for me, and I will add logical definitions to all of these metabolomics terms: CHEBI:16070 CHEBI:16831 CHEBI:15676 CHEBI:17113 CHEBI:16024 CHEBI:48300 CHEBI:16813 CHEBI:24148 CHEBI:18089 CHEBI:2181 CHEBI:16015 CHEBI:16997 CHEBI:15963 CHEBI:33942 CHEBI:17151

[nicolevasilevsky]

@pnrobinson I am done adding the new terms, but I still need to add the logical definitions.

I also need to add the annotations to the diseases. The instructions to get the latest version of hp.obo worked great, I was able to get the latest hpo.obo version without issue.

Where I am having issues though is with the workbench. Using the workbench, I can only suggest new annotations, not directly add new annotations, is that correct?

I can directly add new annotations via HPhenote, that you showed me around Christmas time, but that does not have the latest version of HPO. Is there a way to get the latest version of the HPO file in that tool, then I can directly add the annotations.

Thank you!

[pnrobinson]

Hi Nicole, I am going to add a new feature to the workbench that shows disease annotations according to organ system. We should probably rethink the way we are managing annotations and github--either we put this on the main HPO tracker or we use more the annotation tracker. But the current feature can also be used to suggest a new annotation, just change the text in the dialog.

[nicolevasilevsky]

I just added a new ticket via the workbench. Might I suggest some clarifications to the instructions, because I wasn't able to properly follow the instructions the first time. My suggestions are in italics.

Viewing annotated diseases The diseases annotated to a given HPO term (including direct and implied annotations) can be viewed in the browser. If desired, users can limit the diseases to one of the databases, Orphanet, OMIM, or DECIPHER. To find the disease of interest, choose the radio button diseases in the upper left and use the autocomplete field to find the disease, and click on the GO button.

Suggesting new annotations First navigate to a disease of interest as above. Then, click on the New annotation radio button in the upper left. Then use the autocomplete field or the HPO ontology hierarchy on the left to find the term you would like to propose as a new annotation for the disease. Then, click on the Suggest new annotation button on the bottom of the screen to open a new GitHub issue as above. Again, please modify the text to provide information to support the suggestion. You will need your GitHub ID and password to submit a new issue. Use the Report mistaken annotation if you have found an error in the annotations for some disease.

[nicolevasilevsky]

@pnrobinson - is this the workflow you'd like me to use, to create tickets for the new annotations that are needed?

[nicolevasilevsky]

(Apologies for all the questions...!) Some diseases are common diseases, like chronic renal failure. To clarify - I don't need to annotate these, yes?

[pnrobinson]

Hi Nicole thanks!, Let us try to do some items like this. However, for uncontroversial new disease annotations, we could also use PhenoteFX directly. We can do the first N annotations together. I am going to release a second version of HPO Workbench with a couple of improvements probably in the next few days. I will update the HowTo (which now appears in a new dialog window that shows the read the docs pages) according to your suggestions but I am probably going to revise everything since a few changes were made to the gui.

[nicolevasilevsky]

Ok, we have a call scheduled on Friday, we can review adding the annotations in PhenoteFX together then, or I'll ask Eileen if you have any time this week sooner than that.

Is PhenoteFX different than HPhenote?

[nicolevasilevsky]

@pnrobinson and @drseb I downloaded OWLTools per your instructions in the HPO workbench documentation. Does that mean I could MIREOT terms on my own now? If yes, could you provide me with some instructions of what code to run? (The instructions in the workbench were super helpful!)

[pnrobinson]

Hi @nicolevasilevsky I have expanded the entire documentation section, let me know if it works better! I do not know how to MIREOT terms, I think Seb has been doing that the entire time.

[drseb]

@balhoff I regenerated go_import. But since I do not know how to use/setup robot I switched back to my owltools-pipeline. Let me know if go_import is also ok, when generated through this pipeline.

[drseb]

@nicolevasilevsky let me know if there are more requests that I have missed

[balhoff]

@drseb the only import targets I set up for robot so far are ZFA and RO—so you can probably run the GO import target. But I suspect your file is okay, I probably can't test anything until much later today.

[nicolevasilevsky]

@drseb for some reason, I only see some of the CHEBI terms in HP, many of them are still missing. These are missing: CHEBI_16070 CHEBI_16831 CHEBI_17113 CHEBI_4208 CHEBI_48300 CHEBI_16534 CHEBI_18089 CHEBI_2181 CHEBI_16997

[drseb]

well... I was stupid. I re-generated go_import not chebi_import... sorry

[nicolevasilevsky]

No worries! At least it is an obvious fix. :)

[nicolevasilevsky]

@drseb would you be able to MIREOT the CHEBI terms? Thank you!

[drseb]

Let me know if all the classes are available now. Thanks.

[nicolevasilevsky]

@drseb yes, thank you! I added logical definitions to all of these terms.

Reminder, @pnrobinson, as we discussed on the phone today, you will add the local import file with the current version of the ontology to PhenoteFX, and then I will update the disease annotations.

Thanks!

[nicolevasilevsky]

added new terms and created a new ticket in annotation repo https://github.com/monarch-initiative/hpo-annotation-data/issues/174