ontology search and publication lookup don't work in ISAcreator

[maciej-jonczyk]

Hi,

I'm using ISAcreator 1.7.11 on ubuntu (unpacked from zip file downloaded from https://github.com/ISA-tools/ISAcreator/releases).
It works fine, but "ontology search" in "Study Design Type" for example doesn't work.
In my console I've got "Problem encountered setting host configuration for ontology search" error.
I've read about proxy settings, is it required for ontology search?
I don't know how to set proxy.

Similar problem is with publication lookup. It simply doesn't work, either for doi and PubMed id

Best Wishes,
Maciej

[proccaserra]

Hi @maciej-jonczyk

Thx for reaching out.
A couple of things about the java tools.

These should be run in a VM with Java 1.8 (the tool do not run with later versions but this you probably know already :) ).

• Regarding the pb you faced with the 'Study Design Type', the following procedure may solve this issue.

You may have to "refresh" the `Ontology Detail Cache'. To do so, please go the the "Settings" option of ISAcreator on the main menu, and then click the blue "update Ontology Detail Cache" button

I just tried it again it cured the pb for me. Let me if the trick works for you.

• Citexplore based search: the service has been disabled so that function no longer works. Sorry!

all the best
P.

[maciej-jonczyk]

Thank you @proccaserra, I have java 1.8.
I've already updated ontologies and it won't help, at least freshly after update. However after computer restart at least search in "All Ontologies" works, whereas search in "Reccomended Ontologies" won't.
All in all, maybe it solves the issue.

In the meantime I faced other issues (Excuse me, if it should be posted as separate issues).

1. I'm suprised that I can't find the Crop Research Ontology in ontology search. I've tried to import it in "settings > configure ontologies",
   but it doesn't accept obo format.

2. I'm using configuration from MIAPPE ([https://github.com/MIAPPE/ISA-Tab-for-plant-phenotyping]).
   I've filled in fields in the Investigation, there were example values, I've deleted some of them for example altitude and longitude. When I saved it, the investigation (i_* ) file in data directory looked fine but each time I open it in the ISAcreator the deleted values (for example for altitude and longitude) returns.

3. I can see duplication of the "Description of Growth Facility" and "Type of Growth Facility". I've inspected the i_investigation.xml from MIAPPE configuration and in that file this duplication is absent.
   Please see the screenshot of the opened isatab file.
   [Edit 25.03.22] mentioned duplication is not present in freshly created project, it appears after closing and reopening of project.

[proccaserra]

Hi @maciej-jonczyk thank your for reporting these issues.

I was able to replicate 3 but not 2.

Regarding 1, accessing Crop Ontology, as ISAcreator performs lookups on NCBO Bioportal and the Crop Ontology seems to not be available (https://bioportal.bioontology.org/ontologies/CO/?p=summary) , I suspect the API call can not find the resource.

Regarding 3, definitely a 'feature' of ISAcreator, which is caused by the java ISA writer upper casing the words found in ISA fields. But since the ISA configuration used to open the files isn't aware of that, this causes the duplication you see.
A "quick / ugly fix" would be to amend the configuration so it matches the behaviour of the java tool . The issue with that may lead to validation problem with other tools.

This leaves us with the issue of supplied values being discarded, that I was unable to reproduce (I am running the tool on macOS 11.6 with java 1.8).

Apologies for the inconvenience.

[maciej-jonczyk]

Dear @proccaserra, thank you for help.
I've modified the configuration and now there is no duplication.
So I understand, that first letter of all words in field names must be capitalized.

As of problem 2.
I meant I deleted example values for: latitude, longitude and altitude, saved file and when I opened it again the deleted values returned.
I suppose I could just delete that values from configuration, but in this way I will have to modify configuration each time I have a field for which I don't want to provide value.

[maciej-jonczyk]

@proccaserra I've realised that "returning values" is a consequence of default values provided in the configuration file.
So if new value is not provided or default deleted in ISAcreator the default value is set when the ISA-tab file is re-opened.

So I think the only solution is to delete default values in investigation file in configuration.

New problem - Study Design Type
this field requires ontology term. Ontology recommended by configuration file (Crop Ontology) is not available in lookup.
I've set the value manually to "CO_715:0000147" and saved the file. After re-opening of the file "CO_715:0000147" entry was trimmed to "0000147".
Entry of this type was successfully used in "Type Of Growth Facility" so I assume it is not problem with colon symbol.
Here are appropriate entries cut from the configuration file.

[proccaserra]

Hi @maciej-jonczyk , that's correct, expected behavior, this was discussed and the miappe configuration developers felt it was a way to draw the attention to those values and provide. The risk, within the constraints of the tool, is indeed saving the default values.

Regarding the second issue: crop ontology is not longer available from Bioportal and there isn't much I can do here.
So, I presume the miappe configuration should be edited to remove this constraint and let user supply a value of their choosing.
From a user point of view, having to edit the configuration xml isn't that great (!) to get a curie for the term. A better way would be to change the configuration for the data-type for the field is a list and the controlled terms are provided as enum.

Possibly http://purl.obolibrary.org/obo/AGRO_00000360

https://bioportal.bioontology.org/ontologies/AGRO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FAGRO_00000360&jump_to_nav=true

The issue is check if this would break compatibility with MIAPPE and the conversion with BRAPI

Hope this helps.

bw
P

[maciej-jonczyk]

Hi @proccaserra, thank you for the clarification.

As of Crop Ontology, it is defined as preffered in MIAPPE tutorials. However It seems that user can provide entries from other ontology. The current version of MIAPPE 1.1 is from 2019 so maybe it needs an update, I also think AGRO would be proper.

New question
In ISA-creator I can't see the ONTOLOGY SOURCE REFERENCE section. Strangely, it is present in the i_investigation.txt file, both that from MIAPPE and from examples here https://github.com/ISA-tools/ISAdatasets/tree/master/tab. It can be filled in in the file itself (outside ISA-creator), but only at the very end of file editing because the provided values are deleted when saving ISA-tab in ISA-creator.
Also, in ISA-tab documentation for several sections (e.g. INVESTIGATION PUBLICATIONS, INVESTIGATION CONTACTS) there are appropriate Term Accession Number and Term Source REF. They are provided in i_investigation.txt file but they aren't provided in ISA-creator. I see they aren't required by MIAPPE but their absence in ISA-creator is surprising.

EDIT
Allright, now my problem is solved. I have used EFO ontology and I can see it was automatically added in appropriate places in i_investigation.txt file. So it is not intended to be edited manually. It also strengthen the need of Crop Ontology replacement in MIAPPE preferred ontology.

Once again, thank you for your time.
Best Wishes,
Maciej

[proccaserra]

@maciej-jonczyk
as per the crop ontology site. agro would indeed be legit.

option 1: use Agro available from NCBO Bioportal (very little extra work)

option 2: use AgroPortal (essentially a NCBO Bioportal customized to support agronomic research and hosted in Montpellier, Fr.). this would require extending the java code in ISAcreator which handles ontologies to point to right endpoint and obtain an API key from AgroPortal. This is more involved

[maciej-jonczyk]

@proccaserra, allright, I'll use AGRO linked in the ISAcreator ontology look-up.

[DanBerrios]

@proccaserra Hi Philippe. I am using ISACreator, latest release and I also am finding it isn't searching Bioportal ontologies. I tried the Settings->Update Ontologies Detail Cache, but the cmd window shows:

_____populateAcceptedOntologies()____
The BioPortal REST service reports Internal server error
Found 0 ontologies

Do you know why this might be? Thanks