edamontology / edam-browser Goto Github PK

currently HS

It's a small detail, but if it can easily be hacked, it would be much nicer to render "EDAM" instead of "owl:Thing" here:

The links in the browser to bio.tools do not work (for me)

Propositions:

• ajouter une colonne pour EDAMbrowser dans le tableau de comparaison des fonctionnalités
• fournir un lien vers une ontologie 'custom' pour le critère 6
• le terme "getter" n'est pas clair

For instance, the concept information panel lists GFF twice as the parent of the GFF2 concept (see https://edamontology.github.io/edam-browser/#format_1975). It should appear once.

Following discussion with @hmenager it is needed to not onyl show the usage of a term but also its descendants.

For now it only accept uri. It should also accept free text and propose the concept where the given string can be found.

Folks might not be familiar with what "Parent", "Narrow synonym" etc mean, so tool tips here could make a massive difference.

I recently created an "EDAM Format request" issue template which includes some documentation you could use:
https://github.com/edamontology/edamontology/blob/master/.github/ISSUE_TEMPLATE/edam-format-concept-request.md

Note! The markdown includes HTML comments (the useful bit for the tool tips) so you'll not be able to see these in GitHub, until you click the "edit" button (or just download the mark-down and look in a text editor)

cc @hmenager

... as proposed in edamontology/edamontology#326 (comment)

Hi,
I need to issue a DOI for the EDAM Browser, I've been recommended to use zenodo. Could you allow it to use hook ? You probably received an email requesting this acces.
Thanks

In the term-change window the title is not rendering the term correctly:

It seems to be like this for all terms

• OLS
• BioPortaal
• Web Protege
• AberOWL
• Ontobee ?

To help colour-perceptive-impaired people (well me at least) a bit :)

I struggle to see the difference in colour used for Operation and Topic here:

I recall we had a sort-of "formal" colour schema for EDAM as used on Kenzo's EDAM poster, right @hmenager ?

From edamontology/edamontology#299 (comment)
Pending after edamontology/edam2json#4

After suggesting a new concept with EDAM browser, the format of the generated issue should be similar to the following issue templates:

• For formats https://github.com/edamontology/edamontology/issues/new?assignees=&labels=&template=new-format.md
• For data https://github.com/edamontology/edamontology/issues/new?assignees=&labels=&template=new-data.md
• For identifiers https://github.com/edamontology/edamontology/issues/new?assignees=&labels=&template=new-identifier.md
• For operations https://github.com/edamontology/edamontology/issues/new?assignees=&labels=&template=new-operation.md
• For topics https://github.com/edamontology/edamontology/issues/new?assignees=&labels=&template=new-topic.md

indicats that we query tess bio.tools bioweb to know how many ressource have bee, labeled with the given element

• URL parsed
• EDAM version and last edit date -> needs to be added to the JSON export first!

something weird is happening (6643 is obv. not right)

• Data & format annotations:
  Either from https://test.galaxyproject.org or https://usegalaxy.eu (..org released with datatypes update every 4 months; ..eu has a few more tools than ..org).
  Higher priority (cool to do after I get all these updated in the Galaxy code, and adequate updates are released in EDAM)

• Operation & topic annotations:
  Would be the best to pull from the main ToolShed. A minimalistic API implemented to do this would probably suffice for this functionality; otherwise would need to pull info from Schema.org|BioSchemas annotation of the generated HTMLs (which is going to be implemented).

Super-nice to have e.g. a radio button or check-box, which causes bio.tools usage counts to be rendered in the graph:

1. usage of the current term
2. usage of current term + kids (descendants)

something like:

Say I've selected to see "Only Operation", but I'm on a term with links to e.g. Data terms:

In this scenario, clicking on either of the Data links does nothing.

What I suggest it could do is to render the Data branch down the term clicked upon. This is related to https://github.com/IFB-ElixirFr/edam-browser/issues/24.

For now we can only copy the link to browse the EDAM element within the browser, not juste the link

From a need raised by @jvanheld and an idea of @thomasrosnet, add a button something like the copy link when cloning a repo in github

Please add DOIs to the references where applicable. For instance,
https://doi.org/10.1186/s12859-015-0456-9 for https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0456-9 in your bib file this is with no DOI, see below.

@Article{hoehndorf2015aber,
title={Aber-OWL: a framework for ontology-based data access in biology},
author={Hoehndorf, Robert and Slater, Luke and Schofield, Paul N and Gkoutos, Georgios V},
journal={BMC bioinformatics},
volume={16},
number={1},
pages={26},
year={2015},
publisher={BioMed Central}
}

Same is true for other references.

to make it explicit these are the ones previously browsed by the user

Hi, Could you allow travis to run Continuous integration on IFB-Elixir projects ? It can be done at https://github.com/settings/connections/applications/f244293c729d5066cf27 (from there)

Thanks to @matuskalas in #20 (comment) who spot that the count of https://edamontology.github.io/edam-browser/#operation_3198 is wrong for bio.tools.

I think it might be related to the fact that the term is duplicated, and thus counted twice, but when looking at https://edamontology.github.io/edam-browser/#topic_0084 the descendant count make no sens at all for now.

Navigate to this URL https://ifb-elixirfr.github.io/edam-browser/#operation_2928&operation
expand "Operation" node, and then try to expand "Alignment" node. The node does not expand, and there is a JS error:

Uncaught TypeError: Cannot read property 'text' of undefined
    at textAccessorDefault (tree-edam-stand-alone.js:382)
    at interactive_edam_uri (tree-edam-stand-alone.js:318)
    at append_row (tree-edam-stand-alone.js:349)
    at tree-edam-stand-alone.js:239
    at Array.forEach (<anonymous>)
    at standAloneSelectedElementHandler (tree-edam-stand-alone.js:235)
    at tree-edam-stand-alone.js:435
    at attemptToSelectElement (tree-reusable-d3.js:310)
    at browseToFromElement (tree-reusable-d3.js:404)
    at browseToFromElement (tree-reusable-d3.js:410)

This is caused by "d" being undefined at line 382 of https://ifb-elixirfr.github.io/edam-browser/js/tree-edam-stand-alone.js.

E.g., when searching for "calculation", drop-down suggestions list shows the exact match Calculation (operation_3438) at almost twentieth place.

In https://edamontology.github.io/edam-browser/#format_3620 the link behind bioportal is http://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Fformat_3620 whichis not resolved [Edit] found.

http://edamontology.org/format_3620 is resolved to https://bioportal.bioontology.org/ontologies/EDAM?p=classes&conceptid=format_3620

i.e. which completely expands EDAM Topic, Operation, Data or Format subontology - so I can see all concepts for one-click. It's a big chore currently.

This would be hugely useful when using EDAM browser to refactor EDAM.

I first heard this idea from @hmenager I think.

It would be worth experimenting with (an option to render) line weights according to the bio.tools term usage, i.e. the weight of a line from termA to termB would reflect the usage of termA and all it's kids.

The use-case here is using EDAM-Browser to optimise EDAM during refactorings, i.e. we'd benefit greatly from a visually immediately obvious rendering of term usage.

Add the following information texts to the "Terms details" panel (HTML tooltips that appear when hovering an element) to help new users understand it better:

• "Term": "Preferred name for the concept"
• "Definition": "Short definition of the concept"
• "Comment": "Misc. information that may help understand the scope of the concept"
• "Exact synonyms": "Alternative term(s) that represent exactly the same concept"
• "Narrow synonyms": "Alternative term(s) that represent a slightly narrower scope"
• "Broad synonyms": "Alternative term(s) that represent a slightly broader scope"
• "Related synonyms": "Alternative term(s) that represent a closely overlapping scope"
• "URI": "Permanent concept identifier"
• "Parents": "Link(s) to the parent concept(s) which represent broader concepts"
• "Community usage": "Usage of this concept in various databases and registries"
• "bio.tools": "Bioinformatics Tools and Services Discovery Portal"
• "BioSphere": "IFB (ELIXIR France) Cloud Services to analyze life science data"
• "bioweb": "Online catalog of bioinformatics programs and databanks available at the Institut Pasteur"
• "TeSS": "ELIXIR Training Portal"
• "Links": "Links to this concept in other ontology browsers"

There are various suggestions in:
edamontology/edamontology#299

which should be tracked in this repo instead. No easy way to migrate the issue, so please take a look at the above, and close it (and this) once you're happy.

I think some of the stuff in there has already been done, and the rest can be covered by new issue requests in this repo.

Hi Bryan

Just letting you know that EDAM 1.25 is out ... pls. update EDAM Browser.

Thanks!

cc @hmenager

Currently the EDAM URL link is actually linking to the current page in EDAM Browser (not useful) - I'd suggest the link is the same as rendered (which resolves to EDAM concepts in BioPortal currently).

When I click "EDAM...Only Operation" the label "Operation" is clipped:

Hello!
Currently at Montreal University we are developing an ontology for a catalogue of scientific equipment, and your browser seems very useful for the project. Following the schema you propose in https://github.com/IFB-ElixirFr/edam-browser/blob/master/ontology.schema.json we see that an entity can have only a parent, however checking the schema of the EDAM ontology it supports the notion of multiple parents (which are rendered by the browser). As we need to support entities with multiple parents, we are interested how do you feed teh EDAM schema into the browser, so we could adapt our data as well. Thank you!!

Maybe this is an issue just for formats.

For instance, take
http://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Fformat_3727

EDAMBrowser does not show most of the information.

Edit:

Is Identifier Of does not exist yet, and should be created, the others have been done in #174

Original post

The relationships showed in the form should be only the ones for the type of concept considered.
Here's a table of which relationship should be showed, depending on the type of concept the user suggests.
(Please not Is Identifier Of does not exist yet, and should be created).

The text of the URL shown for format_3620 is correct. However, the text cannot be copied and when clicked the URL is https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/ - which is incorrect as the URL.

It is not clear how the correct URLs can be copied.

Currently you can have all or one of the EDAM sub-ontologies rendered via:

It might be nice instead if one could select any combination, by checkboxes

I could imagine e.g. wanting see both Data and Formats at the same time.

Particularly for formats, where the terms are children of both file type family (e.g. "XML") and category ("Sequence alignment"), it would come handy to see them in the box with the details about the term.

Following the question asked on issue #38, where we asked for the possibility of defining multiple parents for an entity in the JSON ontology file, now we are interested to know if it is possible to do it directly in the edam browser. Our interest is to allow users not familiar with JSON to perform such operation. Thanks!

e.g. "Supports EDAM 1.20" with link(s) to http://github.com/edamontology/edamontology and/or https://www.ebi.ac.uk/ols/ontologies/edam and http://bioportal.bioontology.org/ontologies/EDAM.

From UDD. @tillea made a script that pulls all the EDAM annotations from there.

Please contact the debian-med mailing list or @tillea if help needed.

The current interface allows to select terms from the ontology to specify the relationships in a new concept / updated concept proposal.
However, the interface does not filter on concept type (e.g. it is possible to specify a format in the has_topic relationship).
This interface should filter:

• same type for the Parent
• topic for has topic
• data for is format of
• data for has input
• data for has output