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Using dashboards to monitor ontology standardisation and community activity

Charlie Hoyt, Nicolas Matentzoglu, Anita Caron

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Ontology Summit 2023 – 8 February 2023 (https://ontologforum.org/index.php/OntologySummit2023)

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The problem of encouraging and monitoring ontology standardisation/interoperability

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The four layers of Open (Bio/med) Ontology interoperability

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Common formats and tools

ROBOT, OWL API, ODK, rdflib, fastobo, owltools, dosdp-tools etc are able to read and write ontologies in commonly understood formats (RDF/XML, OWL model). Standardising prefixes used in cross references (bioregistry).

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FA[IR]ness & Openness

Ontologies should be findable, accessible and openly available.

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Shared design patterns

DOSDP templates, ROBOT templates, OTTr and other systems serve as tools to abstract modelling patterns and share them across ontologies.

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Shared vocabularies and upper level integration

RO standardises the relationships to be used in OBO ontologies.�OMO standardises the annotation properties to be used for term and ontology metadata.�COB provides the upper layer for biological and biomedical ontologies.�Term-reuse across OBO ontologies.

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How does the OBO Foundry actively engage in the process of facilitating interoperability?

Developing standards for a unified representation of ontologies: COB, RO, OMO

Creating OBO Principles for the development of open and FAIR ontologies

Develop infrastructure for effective and scalable ontology management and quality control: ROBOT, ODK, Dashboard

Building a community that facilitates collective growth and development of shared best practices.

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Examples of concrete problems across OBO ontologies

A lot of variation

in terms of used properties (object properties, annotation properties)

IAO:issue tracker item vs rdfs:seeAlso for linking GitHub tickets
IAO:term editor vs dc:contributor
oio:date vs dc:date

versioning habits
representation - and thus interpretability - of cross references and other mappings

How “active” and “responsive” are ontologies to deal with requests

new terms
standardisation requests

Chaos in prefixes:

Can't tell when to use CURIE as a string vs IRI in many places. E.g., MONDO uses legacy Identifiers.org URIs for HGNC, other resources use CURIEs, etc.
CURIEs not standardized (different dashes, punctuation, capitalization, use of bananas)
CURIEs have unknown prefixes (e.g., CASGEN appears in VTO and TTO, but not clear what it is)

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�This is a tiny selection..

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The OBO principles provide a map towards open, interoperable ontologies

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Some of our favourite principles:

P1) Open - The ontology must be openly available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed in altered form under the original name or with the same identifiers.

P7) Relations - Relations should be reused from the Relations Ontology (RO).

P10) Commitment To Collaboration - OBO Foundry ontology development, .., should be carried out in a collaborative fashion.

Often, their interpretation was down to the community, and therefore variable.

https://doi.org/10.1093/database/baab069

P1) Open - The ontology MUST be openly available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed in altered form under the original name or with the same identifiers.

P2) Common Format - The ontology is made available in a common formal language in an accepted concrete syntax.

P3) URI/Identifier Space - Each ontology MUST have a unique IRI in the form of an OBO Foundry permanent URL (PURL).

P4) Versioning - The ontology provider has documented procedures for versioning the ontology, and different versions of ontology are marked, stored, and officially released.

P5) Scope - The scope of an ontology is the extent of the domain or subject matter it intends to cover. The ontology must have a clearly specified scope and content that adheres to that scope.

P6) Textual Definitions - The ontology has textual definitions for the majority of its classes and for top level terms in particular.

P7) Relations - Relations should be reused from the Relations Ontology (RO).

P8) Documentation - The owners of the ontology should strive to provide as much documentation as possible.

P9) Documented Plurality of Users - The ontology developers should document that the ontology is used by multiple independent people or organizations.

P10) Commitment To Collaboration - OBO Foundry ontology development, in common with many other standards-oriented scientific activities, should be carried out in a collaborative fashion.

P11) Locus of Authority - There should be a person who is responsible for communications between the community and the ontology developers, for communicating with the Foundry on all Foundry-related matters, for mediating discussions involving maintenance in the light of scientific advance, and for ensuring that all user feedback is addressed.

P12) Naming Conventions - The names (primary labels) for elements (classes, properties, etc.) in an ontology must be intelligible to scientists and amenable to natural language processing. Primary labels should be unique among OBO Library ontologies.

P16) Maintenance - The ontology needs to reflect changes in scientific consensus to remain accurate over time.

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Operationalising OBO principles: Interpretations of the principles is not always clear

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P9: The ontology developers should document that the ontology is used by multiple independent people or organizations.

P1: The ontology must be openly available to be used by all without any constraint other than ...

I have added some links to databases that use my ontology..

Of course I have many users, here is their email.

MIT! Artistic license! Creative commons! Custom..

I made a note in my README.md!

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OBO principles operationalised

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https://doi.org/10.1093/database/baab069

http://dashboard.obofoundry.org/

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Overview of the OBO Dashboard: Standardising metadata across OBO Foundry ontologies

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@matentzn

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OBO Dashboard Demo

http://dashboard.obofoundry.org/

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New Ontology Requests at OBO: General Workflow

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1. Ontology Representative submits issue at the OBO Foundry registry GitHub Repository

3. OBO Reviewer is selected by Committee and provides feedback

2. Ontology is loaded into a special New Ontology Request Dashboard for basic metadata QC

4. OBO Reviewer makes recommendation during OFOC call, resulting in accept/reject

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Managing new Ontology Requests in the OBO Foundry

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Project specific custom Dashboards

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Great, a Dashboard. Now what?

How do we get people to “go green” (fix issues)?

Policies (No-error dashboard a requirement for OBO Foundry Ontology status on 1st Jan 2024)
Training (like today)
Tools (Robot, ODK, bioregistry, curies)
Carrots (Ubergraph, etc)

OBO principles are great, but what �about FAIR?

A lot of our efforts, including GUPRIs, �metadata standardisation, etc are �intrinsically related
We need to work across standardisation �efforts (FAIR Impact, OBO, Elixir, �FAIRisFAIR) to influence data managem.�plan requirements of our grant orgs

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https://agroportal.lirmm.fr/

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Dashboards for standardising metadata

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@cthoyt

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Ontology Quality Assessment Toolkit (OQUAT)�https://cthoyt.github.io/oquat

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Ontology Versioning (by Petr Křemen)

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Dashboards for measuring social workflows

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@cthoyt

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https://github.com/cthoyt/obo-community-health

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https://github.com/cthoyt/obo-community-health/contacts

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Using the OBO Dashboard Kit to create your own, customised OBO Dashboard

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@anitacaron

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Customized OBO Dashboards

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Dashboard Template

Custom Dashboard

Create from template

dashboard-config.yml

configure

configure GH pages

dashboard.yml

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Run action

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Inspect Dashboard

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https://oboacademy.github.io/obook/howto/deploy-custom-obo-dashboard/

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Acknowledgements

Funding

Defense Advanced Research Projects Agency (DARPA) award W911NF2010255 (PI: Benjamin Gyori)

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