isa-tools / msio Goto Github PK

Metabolomics Standards Initiative Ontology

Java 89.24% Shell 2.86% Batchfile 0.19% Makefile 7.71%

metabolomics fluxomics mass-spectrometry nmr-spectroscopy data-science data-sharing

msio's Introduction

Metabolomics Standards Initiative Ontology (MSIO)

MSIO aims to provide a single point of entry to support semantic markup of experiments making use of NMR and MS techniques to identify, measure and quantify small molecules known as metabolites. MSIO covers metabolite profiling, targeted or undertargeted, tracer based applications. MSIO reuses a number of resources such as CHEBI, DUO, NMRCV, OBI, and STATO.

It is compatible with OBI and can be imported in it but also can be used as is for users working solely on Metabolomics.

The following screenshots allow for a sneak peak at the resource to gauge its coverage.

Material Processing:

Data Transformation:

Material Entities:

Information Entities:

Versions

The development version of the ontology is at: MSIO-edit.owl

msio's People

Contributors

Stargazers

Watchers

Forkers

msi-metabolomics-standards-initiative jmillanacosta

msio's Issues

Fail to load MSIO-edit.owl

Hi,

I tried to load MSIO-edit ontology, but fail to load imported nmrCV ontology at:

MSIO/MSIO-edit.owl

Line 19 in e826b12

<owl:imports rdf:resource="http://nmrML.org/nmrCV"/>

Add missing definitions

for terms:

manufactured by (MSIO_0000183)
HPLC instrument (MSIO_0000161)
fermenter (MSIO_0000167)

“Illegal redeclarations of entities” when loading into Protégé

When loading the MSIO-edit.owl ontology into Protégé, the following error occurs (once).

Level: ERROR
Time: 1533309437054
Message: Illegal redeclarations of entities: reuse of entity http://usefulinc.com/ns/doap#bug-database in punning not allowed [AnnotationProperty: bug-database, ObjectProperty: bug-database]

Replace MSIO:organization (MSIO_0000020) by reusing OBI:organization (OBI_0000245)

Remove msio:organization (MSIO_0000020) (no need to deprecate as the ontology is not yet live)
MSIO defines device as equivalent to 'manufactured by' only organization; this should be replaced by subClassOf (and relying on obi:organization)
MSIO declares the individual Thermo Scientific with type organization; use obi:organization and declare types for the other relevant individuals

Add definitions for organization individuals

The following individuals are missing definitions.

http://purl.obolibrary.org/obo/MSIO_0000068
http://purl.obolibrary.org/obo/MSIO_0000093
http://purl.obolibrary.org/obo/MSIO_0000097
http://purl.obolibrary.org/obo/MSIO_0000098

Integration of MSIO in EBI Ontology Lookup Service

@proccaserra
in order to be able to use MSIO parent terms in our cv-mapping file for mzTab-2 for metabolomics, we need to be able to resolve child <-> parent relationships. I currently use the EBI's OLS for that, however, MSIO is not available there (yet).

Alternative: if I can query another resource to resolve MSIO terms for me that would also work.

Current Lookup Service

'metabolite quantitation using high performance liquid chromatography' (MSIO_0000099)
'trifluoroacetylation' (MSIO_0000113)
'chromatography column' (MSIO_0000160)

Replace msio:metabolite (MSIO_0000035) with chebi:metabolite (CHEBI_25212)

I'll implement this replacement by:

Remove the class msio:metabolite (http://purl.obolibrary.org/obo/MSIO_0000035) - no need to deprecate the URI at the moment as the ontology is not live.
Expand the CheBI import to include role, biological role, biochemical role, and metabolite - I'm including manually the whole hierarchy as we don't want the intermediate classes for the chemical entities.
Replace the axiom in the metabolite pool size estimate class about metabolite, changing subClassOf 'is about' some (metabolite or pathway) to 'is about' some (pathway or has_role some metabolite)

Fix URIs

Multiple entities still have URIs of the form:
http://www.semanticweb.org/prs/ontologies/2013/11/MSI_AO.owl#SIRMS0000004
and need to be changed to MSIO URIs.

Other URI issues (e.g. MSIO_0000102) also need fixing.

Add definition for 'extracellular flux' (MSIO_0000151)

The definition for extracellular flux (http://purl.obolibrary.org/obo/MSIO_0000151) is currently missing.