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RecentUpdates
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RecentUpdates
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**Updated Jun 14, 2018:
New version (version 1.5.1b) of MicrO was released.
Removed 6 duplicate classes.
Fixed 4 classes that had identical rdfs labels.
Fixed IRI classnames for several new MicrO classes.
*** Updated Jan 23, 2018:
New version (version 1.5) of MicrO was released.
ChEBI temporary classes were removed and replaced with new ChEBI terms.
A large number of organic carbon fermentation and assimilation assays were added, along with their synonyms, extracted from ~1500 new taxonomic description of Firmicutes using a natural language processing algorithm (MicroPIE v. 2.0).
Logical axioms for commercial diagnostic assay kits (RapID, Vitek, Biolog, API) were checked for accuracy and fine-tuned where necessary.
*** Updated Jan 6, 2018:
New version (version 1.4) of MicrO was released.
ChEBI temporary classes were removed and replaced with new ChEBI terms.
Organic fermentation assay classes were ontologized to match ChEBI terminology.
*** Updated Mar 23, 2016:
New version (version 1.3) of MicrO.owl was released.
Fixed problem of logical definitions of some prokaryotic qualities incorrectly using quality terms, and object properties under 'has quality' incorrectly using quality terms as domain values. Transformed prokaryotic colony qualities into prokaryotic colony (material entities) and modified term definitions. Created parent terms for prokaryotic colony qualities and linked the material entity terms with quality terms using logical axiom 'quality of'. Thanks Ramona!
*** Updated Mar 10, 2016:
New version (version 1.2) of MicrO.owl was released.
Fixed some minor issues with definitions and logical axioms for a handful of classes in response to reviewer's comments on the manuscript (Blank et al., J Biomedical Semantics, in review).
*** Updated Feb 10, 2016:
New version (version 1.1) of MicrO.owl file was released.
***Updated December 2015 and January 2016:
Large number of new classes of culture medium recipes (from the DSMZ) were added.
Several issues on the Issue Tracker were solved/addressed (see Issue Tracker).
Additional imported terms from NCBI Taxonomy, DRON, ChEBI, PR, REO, ENVO, and PO were added.
***Updated Dec 1, 2015:
Ontology manuscript submitted to Journal of Biomedical Semantics.
***Updated Nov 30, 2015:
Renamed import module files to BSPO_imports.owl
Replaced import files with the URLs of the imports (correcting Tracker Item #5).
Temporary IRIs were replaced with proper purl addresses.
***Updated Nov 29, 2015:
Removed dates in MicrO.owl file and in import modules.
Corrected Tracker Item #9 (Terms with incorrect IRIs).
Corrected Tracker Item #8 (replace # in term IRIs with /)
***Updated Nov 10, 2015:
Added several new classes of trace element solutions, vitamin solutions, microbiological culture media, 'undefined inorganic chemical mixture', 'sea salts', 'fetal calf serum', 'calf serum', 'charcoal filter, 'charcoal filtered seawater'
Am systematically adding all DSMZ medium recipes as classes.
Imported additional terms from Uberon.
Starting the transition of moving away from file names that have the date in them.
Cleaned up logical definitions for culture media (double-checking correct inorganic chemicals).
***Updated Nov 7, 2015:
Regarding OBI harmonization:
Moved classes under 'microbiological diagnostic assay' to parent class 'assay'.
Checked hierarchy of object property relationships. 'uses material entity', 'uses chemical reagent', 'uses culture medium' are indeed nested under OBI's object property 'has specified input'. Likewise, 'produces metabolic product', 'produces enzymatic product', 'produces fermenation product' are nested under OBI's object property 'has specified output'. Changed domains and ranges and definiations of object properties corresponding to 'microbiological diagnostic assay' to 'assay'.
Fixed problem: 'uses chemical reagent' was under 'has specified output' and should have been under 'has specified input'. There were two object properties 'uses chemical reagent' - these were consolidated into one.
Added imported objecte properties 'participates in', 'is specific input of' 'is specific output of'. Moved 'is metabolic substrate of' under OBI parent 'is specified input of'. Moved 'is metabolic product of' under OBI parent 'is specified output of'.
Also:
Added classes 'prokaryotic colony', 'prokaryotic cultured clonal cell population', 'petri dish',' culture tube', 'liquid prokaryotic culture', 'slant culture'. Added several terms from CHMO, ChEBI, NCBI Tax, OBI, and PO. Added several new terms associated with medium ingredients derived from blood. Added several new classes of microbiological culture media, trace element solutions, and vitamin solutions.
Cleaned up object property class relationships. Streamlined logical axioms in microbiological medium ingredients and clarified names of some object properties.
***Updated Oct 15, 2015:
Added some additional microbiological culture medium recipes (basal cellulolytic medium, sporocytophaga medium, anaerobe basal agar, PYG broth). Added Balch trace element solution and several new temp classes to be added to ChEBI. Clarified a few logical axioms regarding cellulose as microbiological culture medium ingredients. Added several new classes of undefined organic chemical mixtures and revised logical axioms. Added trans-aconitate asimilation assay, aconitate assimilation assay, alph-aminobutyrate assimilation assay, and polyethylene glycol assimilation assay, beta-glucuronidase assay with 4-MU, 6-phospho-beta-galactosidase assay, 6-phospho-beta-galatosidase assay with oNP, alpha-galactosidase assay with 4-MU, beta-glucosidase assay with 4-MU, butyrate esterase assay, hydrolase assay, DNAse assay with indoxyl, DNase assay with pNP. Improved definitions for enzymatic assay classes.
***Updated Oct 14, 2015:
Replaced MicrO Object Property 'has unit' with IAO term 'has measurement unit label'and Data Property 'has magnitude' with IAO term 'has measurement value'. Updated term usages across the ontology.
Added note to README document Notice Regarding IRI Addresses: IRI addresses for imported ontology terms and for MicrO-specific terms are currently temporary. They will be replaced with the correct purl addresses, once a domain name has been approved by OBO (request is pending in the OBO-Discuss-List), and after we have better acquainted ourselves with OBO purl conventions!