isa-tools / ontomaton

OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets.

Version 4:

Version 3:

Version 2:

OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. It has been developed by the ISA Team at the University of Oxford's e-Research Centre.

Read the Publication...

Access the Open Access Bioinformatics article on OntoMaton here.

Eamonn Maguire, Alejandra González-Beltrán, Patricia L. Whetzel, Susanna-Assunta Sansone, and Philippe Rocca-Serra
OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets
Bioinformatics 2013 29: 525-527. doi: 10.1093/bioinformatics/bts718

Please, note that at the time of the publication, OntoMaton was powered by the NCBO BioPortal web services. Since then, we have made the following extensions:

• we upgraded the code to Google Add-ons for Docs and Sheets, which deprecated the Apps Script applications and the Script Gallery, used in the original OntoMaton version
• we upgraded to the new BioPortal API for searching ontology terms and annotator services (see BioPortal 4.0 release notes), as the old API was deprecated in 2014
• we extended the ontology search functionality to support REST services from the Linked Open Vocabularies and the EBI Ontology Lookup Service, thus now allowing ontology term searches over three separate services.

For more information, see our blog posts on OntoMaton.

Installation

With the new add on infrastructure, installation is very easy.

1. Click on the 'Add-ons' menu item in your Google Spreadsheet:

2. Click on 'Get add-ons...' and then search for 'OntoMaton':

You should get the following result:

Here you can click on the image and read more about OntoMaton:

3. To install, click on '+FREE'. You will need to authorise OntoMaton Add-on to access your spreadsheets and to connect to external services (the ontology search services we support):

4. You'll then have the OntoMaton app installed.

You can access it through the 'Add On' menu option.

Ontology Search

From OntoMaton, you can search three different services within one tool: the NCBO Bioportal, Linked Open Vocabularies and EBI Ontology Lookup Service, and insert the terms in your Google Spreadsheet directly. Full term provenance is recorded for you and later downstream analysis.

Ontology Tagging

With OntoMaton, you can select a number of spreadsheet cells and then 'tag' them. This means that OntoMaton will take the terms in the cells and send them to BioPortal's Annotator service. The results will come back as a list of the free text terms, showing for each all matches in BioPortal.

Configuring OntoMaton - Settings

From the settings screen, you can configure:

• How terms should be inserted in to the spreadsheet when not in 'ISA mode' (where the next columns aren't named 'Term Source REF' or 'Term Source Accession'). The two options are as either as a hyperlink to the term in Bioportal/OLS/LOV or as a term name with the hyperlink in parentheses.
• Restrictions, which specify for zero or more columns (with a name in the first cell), restrictions that should be placed on the search space per each of the ontology lookup services we use (Bioportal/OLS/LOV) E.g. the column 'Label' is restricted to terms from the Chemincal Entities of Biomedical Interest ontology (ChEBI). Please, note that for instance if a column has a restriction over the BioPortal service, the restiction will not have an effect if searching terms with OLS.

Restricting OntoMaton's search space

When you add a restriction using the 'Settings' panel for the first time, a 'Restrictions' sheet will be added automatically. This sheet will have the following column headers: Column Name | Ontology | Branch | Version | Ontology Name | Service. Then you may define for a particular column header in your spreadsheet what ontology should be searched (or list of ontologies) over what service (BioPortal, OLS or LOV). A restriction will only apply if using the corresponding service for search.

Additionally, within one ontology restriction, for BioPortal searches, you can restrict to a particular branch of an ontology, providing a way to further restrict the search space.

An example of a google spreadsheet with such functionality can be viewed here: https://docs.google.com/spreadsheet/ccc?key=0Al5WvYyk0zzmdDNLeEcxWHZJX042dS0taXJPNXpJMHc

Video Tutorial

Access the video tutorial showing how to install and use OntoMaton (version 1) here.

Templates

Templates can be found through accessing them on the google templates site. OntoMaton templates are here.

Questions

If you have any queries, please email us at link. For bug reports, please use the issue page here.

License

This work is licensed through a CPAL license, meaning that any derivitives should carry a powered by OntoMaton logo, shown here.

Merchandise

Fancy an OntoMaton t-shirt? We haven't got any to give away...yet! But...you can buy one of these rather snazzy t-shirts from Spreadshirts for just £15!

ontomaton's Issues

Support multiple ontologies in restrictions for each service

At the moment, we only find the first ontology restricting a field for a particular service. Add support for restricting multiple ontologies for each service.
Functionality requested by Damion Dooley.

Case sensitivity of "Term Source Ref"

The auto insert functionality requires "Term Source Ref" to be in the column heading and unfortunately "Term Source REF" does not work as expected. Searching on the web and from my recollection of the ISA-Tab specification, "REF" is the prefered form, although I am more than happy for the test here to be case insensitive.

ScriptError: You do not have the necessary permission to access the requested document.

Hi,
Now, i am started to use OntoMaton, but everytime I search a term this error appers:
ScriptError: Non disponi dell'autorizzazione necessaria per accedere al documento richiesto.
Translation:
ScriptError: You do not have the necessary permission to access the requested document.

How can i fix this?

server error when using Safari 6.0 (7536.25)

After installing OntoMaton script, I started getting an error message when I open my spreadsheets. With "working..." menu status on the background, the message says:

A server error occurred. Please press 'Reload' in your browser.

As a result, OntoMaton menu option doesn't get loaded and all menu items are greyed out. When I refresh, following the suggestion from the error message, I simply get exactly the same error message and the menu is still inaccessible.

The same error pops up for every new spreadsheet I create. So, essentially, I can't create or edit Google spreadsheets in Safari. Running through OntoMaton setup in Chrome (v. 21.0.1180.75), I didn't have any issues.

Access denied for example sheet

When I tried to access the example sheet as described in the docs

An example of a google spreadsheet with such functionality can be viewed here: https://docs.google.com/spreadsheet/ccc?key=0Al5WvYyk0zzmdDNLeEcxWHZJX042dS0taXJPNXpJMHc

I get an access denied error. I believe that is not meant to be this way.

Cheers

Update to OLS4 if needed

Hi,
on 30.10.2023 the OLS system will be upgraded to OLS4. Website promises:

Migrating to the OLS4 API should be as simple as replacing ols with ols4 in the path. For example,
    http://www.ebi.ac.uk/ols/api/ontologies (before)
    http://www.ebi.ac.uk/ols4/api/ontologies (after)

Otherwise the OLS4 tracker with already a few caveats is at https://github.com/EBISPOT/ols4/issues
Yours,
Steffen

Upgrade to LOV API v2

http://lov.okfn.org/dataset/lov/api/v2/

documentation:
http://lov.okfn.org/dataset/lov/apidoc/#lov2search

Addition of searches over OLS

Already available in the live version, added by @Zigur

Features

• The ontology id and version id are bioportal specific, but there is no trace of that when inserted in the spreadsheet. I suggest you use URLs for these identifiers
• Please insert the official URL of the ontology. For example, for a search for "information content entity" the source file is http://purl.obolibrary.org/obo/iao.owl. Most OBO ontologies follow the same convention (namespace -> namespace.owl). Note that more and more (OBO) ontologies have dated PURLs to record version, and ideally these URLs are returned for
• Please add definitions of terms to the interface
• While the title of the ontology is useful, it would be more useful as a hyperlink to their home page.
• I don't know how feasible it is, but you might consider adding headers for the columns that are filled in.
• We encourage attribution at the term level. Please allow for the inclusion of the term editor and term source.

Update documentation

currently available in README file

• instalation

• functionality

'UiApp has been deprecated' Error

When I try to go to the 'About' or 'Settings' menu in Ontomaton, I get the following error:

UiApp has been deprecated. Please use HtmlService instead.

Can this be fixed?

Extend OntoMaton to talk to AgroPortal and SIFR BioPortal

This is a feature request to have an extension of OntoMaton be able to talk to :
http://bioportal.lirmm.fr/
API at : http://data.bioportal.lirmm.fr/

and AgroPortal
http://agroportal.lirmm.fr/
API at : http://data.agroportal.lirmm.fr/

These API are the same than the NCBO BioPortal one. So it should be quite easy to add the feature to OntoMaton. This will extend possible uses of OntoMaton to French (biomedicine) and Agronomy (english).

The only difference in the /annotator API is the format=rdf and score=... parameters.
described in our proxy architecture at:
https://github.com/sifrproject/annotators

Which allows us to develop new features for: the SIFR Annotator, the AgroPortal Annotator and the NCBO Annotator at the same time.

For instance, if you want a NCBO Annotator with score you can talk to :
http://services.bioportal.lirmm.fr/ncbo_annotatorplus/

Still working

Is this tool still working. We want to use it in one of our projects

Problem encountered searching in BioPortal.

Last week I was able to use the plugin, after BioPortal 4.10.

Did the plugin break?

Error message: Problem encountered searching in BioPortal.

Wrong =HYPERLINK() syntax

Hi,
when adding a term, Ontomaton will insert
=HYPERLINK("http://purl.obolibrary.org/obo/MS_1000702","micrOTOF")
which results in a parsing #ERROR complaint by google.
The correct content will be using a semicolon instead:
=HYPERLINK("http://purl.obolibrary.org/obo/MS_1000702";"micrOTOF")

Fixing will need changes in

OntoMaton/OntologyTagging.gs

Line 187 in ca7c340

sheet.getRange(row, selectedColumn).setFormula('=HYPERLINK("'+ ontologyObject.accession +'","' + ontologyObject.term + '")')

and

OntoMaton/OntologySearch.gs

Line 320 in ca7c340

sheet.getRange(row, selectedColumn).setFormula('=HYPERLINK("' + ontologyObject.url + '","' + ontologyObject.term + '")')

Yours,
Steffen

Restrictions over searches on LOV seem not to be working

use case: set a restriction for a column using OBI ontology from BioPortal, the restriction does not apply when searching for 'investigation' in LOV within that column

Add 'apply and close' botton

To all widgets, so that is more obvious after the selection is done.

make ontomaton aware of ISA-Tab templates

if ontomaton detects an ISA investigation worksheet, test for "ontology source reference", and have ontomaton to add the relevant resource to the resource

Feature: add service.tib.eu/ts4tib as OLS endpoint

Hi,
https://service.tib.eu/ts4tib/ is a Terminology Service (TS) building on the OLS software system, including an API that is OLS compatible.
While OLS is mainly targeting the life-sciences, the ts4tib provides a Terminologies for many more disciplines.

We'd like to submit a PR that will add the TS to OntoMaton.
TS API Documentation: https://service.tib.eu/ts4tib/swagger-ui.html

Yours,
Steffen

Fix display 'restriction added' message

Prompt 'tagging' + result tree open directly

When selecting 'autotag' from meno, we do not want the user to have to click again the 'tag' button from the widget but the action should occur automatically. Also when results are found the tree should be open displaying the hits.

404 error when trying to open document

If I click the "use it now" button on the ita-tools page, I get a 404 error.

Display hyperlink to ontology terms in cell

Adding =hyperlink("http://www.ebi.ac.uk/efo/EFO_0001739";"investigator") instead of
investigator(http://www.ebi.ac.uk/efo/EFO_0001739)

Add support for a new setting placing 'term' and 'accession' in consecutive rows

currently, we support 'term'/'accession' in consecutive columns or single cell with hyperlink

Hyperlink error

Hello,

ERROR! in the spreadsheet cell is raised when tagging terms with "Place hyperlinked term name in field" option selected.

The formula inserted in the cell contains a comma:
=HYPERLINK("http://semanticscience.org/resource/SIO_000173","affiliation")

while it should contain a semicolon (manually correcting to semicolon restores the hyperlink):
=HYPERLINK("http://semanticscience.org/resource/SIO_000173";"affiliation")

Not sure if some sort of bug, or if it depend on local language settings (Italian).

How do I get OntoMaton to show up in Add-ons in a Googlesheet?

How do I get OntoMaton to show up when I search for OntoMaton from Add-ons in a Googlesheet?
I downloaded and opened the tar file but then what?

Add support for restrictions for the annotator functionality.

Requested by Damion Dooley.

We currently support restrictions for the search functionality only. Allow to restrict the ontologies used by the annotator too. API documentation here: http://data.bioontology.org/documentation#nav_annotator

Change 'Term URI' and add service in Terms sheet

include just uri rather than id (onto_abbrev:uri); also add service

itemDefinitionHandler missing from github

Hi guys,

Really finding this tool useful. Thanks very much. We modified it to insert ONTO:00012345 rather than purls which don't help when we are trying to load the experiment data into Chado.

What's happened to itemDefinitionHandler() ? I can't find the code for it anywhere on GitHub - although I can find it in Utils.gs on my local copy.

We found that this is essential (try looking up "London" in GAZ) but seems broken. I am trying to fix it - will post what I find.

cheers,
Bob.

the Biological Collections Ontology in BioPortal seems not included in search results

pb with settings in Ontomaton

caused by:
Request failed for http://lov.okfn.org/dataset/lov/api/v1/vocabs returned code 404. Truncated server response: <m... (use muteHttpExceptions option to examine full response).

If term sheet not added, and term selected, the term isn't inserted into the annotation column, just the terms sheet is populated

This is due to the ordering of the operations.

Problems with SNOMED in Ontomaton

Hello,

SNOMED Clinical Terms is missing from Ontomaton search results. SNOMED Clinical Findings does appear, but if I click on 'Details' for a term, I get the following error message:

Error encountered: Request failed for http://rest.bioontology.org/bioportal/concepts/43051?conceptid=http://ihtsdo.org/snomedct/clinicalFinding#65209002&apikey=fd88ee35-6995-475d-b15a-85f1b9dd7a42 returned code 403. Server response:

/bioportal/concepts/43051
2013-07-19 08:02:13.488 PDT
Forbidden
A valid API key is required to call REST services. Please visit http://bioportal.bioontology.org/account to get your API key.
403

I also receive this error when I click on details for a term from SNOMED Test Findings and SNOMED Morphologically Abnormal Structure.

Faith

Detect hidden columns