carrineblank/micro

A Microbial Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions

MicrO

An Ontology of Prokaryotic Phenotypic and Metabolic Characters, version 1.5.1b (released Jun 14, 2018) .

Created by Carrine E. Blank, University of Montana, fall 2013 through spring 2016. Co-contributors and advisors: Hong Cui (University of Arizona), Lisa Moore (University of Southern Maine), and Ramona Walls (University of Arizona).

Includes terms and term synonyms extracted from > 3,000 prokaryotic taxonomic descriptions, collected from a large number of taxonomic descriptions from Archaea, Cyanobacteria, Bacteroidetes, Firmicutes, and Mollicutes.

The ontology and the synonym lists were developed to facilitate the automated extraction of phenotypic data and character states from prokaryotic taxonomic descriptions using a natural language processing algorithm (MicroPIE). MicroPIE was developed by Hong Cui, Elvis Hsin-Hui Wu, and Jin Mao (University of Arizona) in collaboration with Carrine E. Blank (University of Montana) and Lisa R. Moore (Macquarie University).

Contains ~ 3,660 terms and term definitions, along with thousands of term synonyms. Constructed in OWL Protégé; following OBO Foundry principles. Imports over 13,600 terms from 20 other external ontologies, including Phenotype Quality (PATO), the Gene Ontology (GO), and Chemical Entities of Biological Interest (ChEBI) using import modules. Contains over 29,600 logical axioms connecting entities and processes across multiple ontologies to facilitate inference of higher-order phenotypic traits.

Please cite: Blank CE, Cui H, Moore LR, Walls RL. 2016. MicrO: An Ontology of Phenotypic and Metabolic Characters, Assays, and Culture Media Found in Prokaryotic Taxonomic Descriptions, Journal of Biomedical Semantics 7:18. DOI:10.1186/s13326-016-0060-6. https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0060-6

Thanks to Chris Mungall (LBNL), Elvis Hsin-Hui Wu (University of Arizona), Gail Gasparich (Towson University), and Gordon Burleigh (University of Florida) for comments and/or assistance with ontology construction and compilation of taxonomic descriptions.Many thanks to Oliver He (University of Michigan) for technical assistance with OntoBee and OntoFox, and Gareth Owen (ChEBI project leader, head curator) and other curators at ChEBI for assistance in the incorporation of microbial-specific chemical terms and synonyms into ChEBI.Thanks also to the instructors (Melissa Haendel, Matt Yoder, Jim Baihoff) and students of the 2013 NESCent Ontologies for Evolutionary Biology workshop, and to Karen Cranston (NESCent director) and the support staff at NESCent.

This work was supported by a grant from the National Science Foundation Assembling the Tree of Life Program (DBI-1208534), and by a travel grant to attend the 2013 NESCent Ontologies for Evolutionary Biology workshop.

TO DOWLOAD

1. Download the MicrO.owl file in the folder "MicrOandImportModules"

2. Execute MicrO.owl using Protege v. 4.3 or Protege v. 5.0.0 (runs in beta 17).

3. Once executed you can then run the reasoner.

4. You must have a live internet connection when you open MicrO.owl in order to properly download and access all the ontology import modules.

micro's Issues

Definition source annotations on 'R2A agar' and 'R2A medium' have "25 °c" set as the language

Terms with incorrect IRIs

There are a number of MicrO classes and properties that have incorrect IRI prefixes. For example:

http://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#MicrO_0001246
http://purl.org/obo/owl/OBO_REL#MicrO_0001318

There aren't that many of them, so probably best to fix by hand.

bacterial thykaloid part of some electromagnetic radiation

Casually looking at some ontologies and noticed this.
To check for others add axiom: immaterial entity has part only immaterial entity.

Adopt release procedures

Suggestion: separate the "edit" version of the ontology from the currently released production file. Additionally give each release an owl:versionIRI value which is resolvable and remains permanently available. The framework in @cmungall's ontology-starter-kit may be useful.

replace # in term IRIs with /

I can change the prefix for all IRIs at once in Protege, but cannot switch from # to /. This will have to be done in text editor and then check, unless there is a way to do it with owlapi

Duplication of 'environmental material'

Hello!
Looks like you have a duplication of environmental material

The one asserted under environmental feature should be removed along with its subclasses.

colont as a PCO term

I was going to file an issue saying colony should be a term in PCO (and I think it should be), but now I see it is imported from IDO. Therefore, we will need to coordinate this with IDO. I am just recording this here so I don't forget.

New IRI for micro.owl

The OBO foundry PURL request has been approved, so we the ontology IRI of the main file should be changed to http://purl.obolibrary.org/obo/micro.owl (without a date). I a working on this and the import file IRIs in a branch.

MICRO using some malformed IDs

https://purl.obolibrary.org/obo/ENVO_01000542
https://purl.obolibrary.org/obo/ENVO_01000543
https://purl.obolibrary.org/obo/ENVO_01000544
https://purl.obolibrary.org/obo/ENVO_01000545
https://purl.obolibrary.org/obo/ENVO_01000546
https://purl.obolibrary.org/obo/ENVO_01000547
https://purl.obolibrary.org/obo/ENVO_01000548
https://purl.obolibrary.org/obo/ENVO_01000549

An example of a correct IRI is (no https!):
http://purl.obolibrary.org/obo/ENVO_01000549

Context:
https://github.com/orgs/OBOFoundry/projects/5

MicrO in FAIRsharing

Dear Dr Blank and the MicrO Team,

I’m contacting you on behalf of FAIRsharing[1], the online registry of scientific data standards, databases and policies. Our aim is to make your resource as visible as possible to as large an audience as possible. We have emailed you a few times since July via [email protected] but have not yet had a response.

We have a FAIRsharing record for your resource[2]. To ensure our information is as correct and up to date as possible, would you or someone from your team quickly scan the record[2] and ‘claim’ it? (To claim, see link [3] below.) In addition, if the resource is no longer in use and should be deprecated, then we can represent that information as well. If we don't hear back from you in the next couple of weeks, we will mark the resource as Uncertain within FAIRsharing.

Claiming a record as either a group/institution or an individual also gives you the opportunity to make changes to the record yourself, allowing you complete control over how your resource is displayed in FAIRsharing. In addition, if you claim a record(s) as an individual, you can link the record to your ORCID.

FAIRsharing is about making your resource discoverable to a variety of users, such as journals and publishers, researchers and service providers, research and infrastructure projects and programmes, as well as curators, librarians, funders and other policy makers and data scientists[4]. A contact is essential should they have any questions about your resource.

Best wishes,
Allyson

[1] https://fairsharing.org, https://doi.org/10.1038/s41587-019-0080-8
[2] https://doi.org/10.25504/FAIRsharing.brhpb0
[3] https://fairsharing.org/own/standard/claim/bsg-s000784
[4] https://fairsharing.org/communities

Update deprecated ENVO terms.

MicrO needs to do a refresh of its ENVO imports as it is currently listing outdated/deprecated ENVO terms on services like OLS as if they are not deprecated. This is not limited to the example term below, as most if not all of this "food product" branch was deprecated in ENVO for FOODON terms >= 4 years ago. This can create confusion for users looking up terms to tag their metadata.

MicrO version of "pork chop" [ENVO_00003079] via OLS look-up

ENVO version of "pork chop" [ENVO_00003079] via Ontobee look-up

floating UBERON term

UBERON_0007379 has not axioms nor parent class. Perhaps an import error?

Use of CHEBI role

Are you sure you want to assert that things like IDO:symbiont role are subclasses of CHEBI:role?

In IDO, it (and other IDO roles) are subclasses of BFO:role

Incorrect use of xsd:int datatype for string label

    <!-- http://purl.obolibrary.org/obo/MICRO_0001179 -->

    <owl:DatatypeProperty rdf:about="&obo;MICRO_0001179">
        <rdfs:label rdf:datatype="&xsd;int">has cell width</rdfs:label>
    </owl:DatatypeProperty>

I am surprised the OWLAPI even parses this. This may be the reason MICRO is empty on OntoBee

Known Issues

1. Logical axioms for three classes of microbiological culture media are not functioning.
2. There are a number of new terms that are being requested for entry into ChEBI. Temporary terms are located under the class "ChEBI terms to be added and processed"
3. External ontologies are currently being imported using temporary owl files (created by OntoFox) in the "MicrO and Import Modules" folder. Once the domain name request has been approved and purl addresses assigned, these will be replaced.

Punning are preventing from importing terms from MicrO

Hi,

There are a number of Illegal redeclarations of entities in MicrO. This is preventing me from using robot to extract and merge terms from MicrO.

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

Environment classes in MICRO

Preventing domain creep may be useful when possible. The definitions of planktonic environment and periphytic environment look like they could be problematic.

Please feel free to post new term requests on the ENVO tracker. Even if you decide you want the term to live in MICRO, we can perhaps offer some interesting discussion.

egg, egg yolk

Are these correct in the context of microbes?
Are egg and 'egg yolk' 'embryonic structure' for microbes?
Is 'blood clot' 'organism substance'? Microbes don't have blood.
We should review anatomical entity branch.

Add link to publication to readme file

If you google search "micro ontology" you end up at this site (at least I do). Therefore, it would be good to have a link to the new publication in the main readme file.

https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0060-6

Passaging terms

We at OBI are wondering if this ontology is taking new term requests. We are interested in introducting terms about passaging.

References:
infectious-disease-ontology/infectious-disease-ontology#5
https://en.wikipedia.org/wiki/Serial_passage

Fix IRIs of imported ontology subsets

The imported ontologies still have ontofox IRIs, so they don't resolve when the ontology is opened in Protege. They should either use obo foundry purls or direct links to the github location.

Nesting incorrect for measurement of pH growth assay

'pH growth assay'
 and ('uses chemical reagent' some 
    ((hydron
     or hydroxide)
     and ('has quality' some 
        (acidity
         and (
              ('has measurement' some ('has unit' value pH))
         and  ('has magnitude' value 5.0))))))

I believe the intent is that the magnitude is a property of the measurement, not the quality. Consider reaching out to the OBI people for descign patterns here.

Morphology

Need to add:
Ring-like, or ring-shaped

Use of ENVO:habitat as a superclass for MICRO:'subaerial prokaryote habitat'

ENVO differentiates habitats from environments in that the former are environmental systems that can support the life of and allow the growth of a population of some (usually species-level or OTU-level) taxon. For this to work here, one would have to assert that 'subaerial prokaryotes' have such a quality. I'm not sure that's wise, as many of them would just happen to be there in the long tail of the abundance distributions.

Also, the exact synonyms seem a little strange in that they sound more like qualities or dispositions:

Many equivalence axioms should be translated to subclassOf axioms

e.g.

antimicrobial resistance assay:
EquivalentTo
'antimicrobial assay'
 and ('uses chemical reagent' some 'chemical entity')

You can see the consequences of this, e.g. look at ''growth factor requirement assay' after turning on the reasoner

Version field contains full description

The description of this ontology is appearing in the version field in the source data

Unfortunately, this is propagated through to the EBI OLS. I just messaged the EBI twitter account (https://twitter.com/cthoyt/status/1353697667839356929) to alert them. Maybe they can provide a downstream fix, but it would be best if this could be addressed here in the ontology.

Use PURLs for imported files

Currently imports are referenced via GitHub-specific URLs such as https://raw.githubusercontent.com/carrineblank/MicrO/master/MicrOandImportModules/BFO_imports.owl. It would be good to create PURLs for these such as http://purl.obolibrary.org/obo/micro/imports/BFO_imports.owl

develop a set of editing and release SOPs

You can look at what BCO does (https://github.com/tucotuco/bco/wiki), but that is only partially worked out and still has lots of manual steps. Probably better for us to look at what ENVO is doing and try to emulate some of that. We don't have to do it all at once, but we will at least need a basic release policy for the publication submission.

Multiple inheritance: habitat (ENVO_00002036)

Seems like there's a MICRO assertion that a habitat is a biome, which isn't the intended semantics in ENVO. This also creates avoidable multiple inheritance.