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[bioontology-support] [BioPortal] Feedback from Maria Herrero

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Sep 30 12:05:18 PDT 2019


Hi Maria,

I looked at one example in BioPortal from the list of fields that you gave below. I chose the "alpha-1-acid glycoprotein 1” class from your DINTO ontology:

http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582&jump_to_nav=true<http://bioportal.bioontology.org/ontologies/DINTO/?p=classes&conceptid=http://purl.obolibrary.org/obo/dinto_3582&jump_to_nav=true>

… that uses “has substrate”. The “has substrate” field is populated with 14 values in the BioPortal user interface:


[cid:76E891F5-138D-4632-99ED-49565669E836 at stanford.edu]


I double checked this against the contents of the CSV file that we generated. To follow is a screen shot from Excel where the line for the above class is shown. The column for has_substrate does contain all 14 values (separated by the pipe character) of class IDs that were used to populate this field:


[cid:1EF08DC2-6F0C-4283-B8AE-97F3B30EAD55 at stanford.edu]


It appears in this case the the CSV content matches what BioPortal serves, both in the user interface and via our REST API [1]. Could you provide us with a specific example of a class where you’ve detected empty fields that you think are incorrect?

Kind regards,
Jennifer

[1] http://data.bioontology.org/ontologies/DINTO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fdinto_3582?include=prefLabel,properties&display_links=false&display_context=false<http://data.bioontology.org/ontologies/DINTO/classes/http://purl.obolibrary.org/obo/dinto_3582?include=prefLabel,properties&display_links=false&display_context=false>


On Sep 30, 2019, at 7:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Maria Herrero

Email: maria at ebi.ac.uk<mailto:maria at ebi.ac.uk>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FDINTO

Feedback:

Dear colleagues,

Thank you very much for publishing our ontology DINTO on your website and making it available for the public.
We have been recently using the CSV file that you published in BioPortal for our latest version DINTO 1.3. to load a graph database, in which we have also implemented some rules for the inference of new relationships (unknown DDIs) between entities.
This CSV version of the ontology is very useful, however, during the process we observed that some fields in the CSV are empty. They are very important for our project and we would like to know if it would be possible for you to look into the reason for these fields to be missing. In particular, we really need the following fields:

carries
facilitates
has DDI effect
has participant
has substrate
impairs
is carried by
is DDI effect of
is facilitated by
is impaired by
is participant in

We would really appreciate if you could help us with this by creating a new CSV from DINTO 1.3 with values for these fields.

Kind regards,
Maria Herrero
maria at ebi.ac.uk<mailto:maria at ebi.ac.uk>
maria.herrero at kcl.ac.uk<mailto:maria.herrero at kcl.ac.uk>

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