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Add elemental symbols as synonyms to facilitate searching

For new term requests, please provide the following information:

Preferred term label

Observation

Synonyms

examination, measurement

Textual definition

The action or process of observing a phenomenon or event.

Suggested parent term

Operational

Attribution

0000-0003-1023-6239

For the documentation section on synonyms @jaclynsaunders asked if I could:

add a bit more to this? Maybe link out to docs on these conventions.

@jaclynsaunders unfortunately I wasn't able to find any obvious docs explaining this when I wrote it. I tried to come up with concise simple examples to explain it as best I could base on many conversation with OBO people. I think this section gives concise example to understand the concepts, but if it's not clear then let me know more specifically how I can improve it. I could try writing out a more verbose explanation based on my understanding of those SKOS concepts.

For new term requests, please provide the following information:

Preferred term label

Transmission

Synonyms

Textual definition

The passage of something from one entity or location to another.

Suggested parent term

Quantifier

Attribution

0000-0003-1023-6239

As discussed with @jaclynsaunders I'll need to figure out how to add out quantifier/subquantifier, etc relations into BCO-SM so the UI can pull from these instead of maintaining a separate json list of pairing. Todo after #6.

For new term requests, please provide the following information:

Preferred term label

Time

Synonyms

Can use: http://purl.obolibrary.org/obo/PATO_0000165

Textual definition

Use PATO definition or:
A nonspatial continuant that is measured in terms of a sequence of events.

Suggested parent term

Operational

Attribution

0000-0003-1023-6239

As discussed with @jaclynsaunders add new units system to BCODMONT so she can incorporate it in the UI. This should be very straightforward to do.

For new term requests, please provide the following information:

Preferred term label

Release

Synonyms

skos:closeMatch http://purl.obolibrary.org/obo/ENVO_01000975

Textual definition

The release of organisms that have been captured or caught.

Suggested parent term

Ecology > population > release

Attribution

0000-0003-1023-6239

I tried to import NCBITaxon as is done in the PO makefile

mirror/ncbitaxon.owl: 
	$(OWLTOOLS) $(OBO)/ncbitaxon/subsets/taxslim.obo --remove-annotation-assertions -l -s -d --remove-dangling-annotations  --set-ontology-id $(OBO)/ncbitaxon -o $@
.PRECIOUS: mirror/ncbitaxon.owl

Unfortunately I wasn't able to get it to run on a VM with CPU: 6, Mem: 16 GB, Disk: 60 GB.

Can you please update the namespaces to the following:

• Generate a namespace for the schema and upper-level ontology at: http://bcodmo.ocean-data.org/schema/bcodmont with prefix: bcodmont
• For the component ontologies, please have all of the upper level classes made to be subClasses of their associated component names. For example, for anatomy.owl please make the structure owl:Thing > bcodmont:Anatomy > obo:UBERON_0000916 ...
• Generate a namespace for new BSM terms (equivalent to the obo namespaces that we are importing) at: http://bcodmo.ocean-data.org/schema/bsm with prefix: bsm

As mentioned by @jaclynsaunders we have yet to add definitions for many of our new BSM namespace quantifier terms. I'll tackle this when I get a moment.

@kaiiam Add in Dissolved and Particulate. (For @jaclynsaunders - enable floats to be added for dissolved & particulate to specify ranges)

Preferred term label

UTC

Synonyms

skos:closeMatch GMT

Textual definition

Coordinated Universal Time (UTC) is a 24-hour time standard is kept using highly precise atomic clocks combined with the Earth's rotation.

Suggested parent term

Operational > time > UTC

Attribution

0000-0003-1023-6239

As a demonstration of adding new terms into BCO-SM, we will use the following NTR (new term request) from @jaclynsaunders 's recent work which includes the example term: CHEBI:16493, aka 1-deoxy-D-xylulose 5-phosphate.

Examining the term on OLS, we see that the term is subclass to a variety of hierarchies, two of which are shown here:

As explained in the New Term Requests section of the BCODMONT technical docs, we'd check to make sure requested terms isn't yet in the model, then one would create an issue such as this one. Following further along the instructions, note that if an appropriate superclass for a term doesn't exist it may need to be added.

In this example we find the most relevant branch of the Chemistry Compound module, the carbon compound hierarchy.

This is an example of where BCO-SM is a simplification of the imported OBO ontology CHEBI, in which case it is the job of the ontologist to find or create an appropriate superclass term for the newly requested term to be a child of in the BCO-SM model.

In this example, a reasonable course of action would be to also import the term carbohydrate derivative: CHEBI:63299 (in addition to CHEBI:16493 the requested term) to serve as the parent term. If in such a case the intermediate term would only have one child term then it might not make sense to import. Ontology hierarchies with single node intermediates a -> b -> c,d... can be a sign that the intermediate might not merit be it's own term.

In this case however, we also know that other carbohydrate derivative terms such as CHEBI:28681 N,N'-diacetylchitobiose will also be requested. Thus adding the superclass concept carbohydrate derivative to BCO-SM might be a reasonable course of action.

A logical place to insert carbohydrate derivative into BCO-SM would likely be as subclass to carbohydrate. Thus as a result of this issue we'll add the following new terms to the BCO-SM carbohydrate hierarchy:

carbohydrate
   carbohydrate derivative
      1-deoxy-D-xylulose 5-phosphate
      N,N'-diacetylchitobiose

as discussed with @jaclynsaunders I'll try to in the next 2-3 weeks finish the bio modules and write docs for adding new modules.

As discussed Aug 8th (and previously) with @jaclynsaunders we decided to make a new robot template for terms like

dissolved inorganic carbon
dissolved organic carbon
dissolved organic phosphorus
particulate inorganic carbon
particulate organic carbon
particulate organic nitrogen

The goal being to have unique IRI's for these frequently used combinations, which ideally link to back to axioms which can generate the same RDF as if they were created piecemeal using the BCODMO-semantic model phrase.

https://www.ncei.noaa.gov/products/coastal-marine-ecological-classification-standard#:~:text=The%20Coastal%20and%20Marine%20Ecological,standard%20format%20and%20common%20terminology

Suggest removing the following from Operational as they are not in line with the model. Can more richly describe using other component parts in the ontology.

http://purl.obolibrary.org/obo/BSM_0400010
http://purl.obolibrary.org/obo/BSM_0400012
http://purl.obolibrary.org/obo/BSM_0400011
http://purl.obolibrary.org/obo/BSM_0400009
http://purl.obolibrary.org/obo/BSM_0400008
http://purl.obolibrary.org/obo/OBI_0001619

Hey @kaiiam I noticed we don't have anything about mortality, I have some fish datasets where it's binary alive/dead counts of various expressed as TRUE or FALSE or similar. Can we have terms for alive and dead or something to that effect. I don't need it super urgently but when you get to this it'd be great to have.

Thanks!

Not urgent but as discussed March 7th 2022, we decided we'll eventually need the ability to deprecate terms in the templates. In theory it should be as simple as adding one column to each template with something like owl:deprecated in the robot header line.

As the following are all quantitative properties, these can all be moved from Physical/Characteristic to Quantifiers to stay consistent with the model. The UI has been adjusted to handle this move.

http://purl.obolibrary.org/obo/PATO_0000008 does not appear to have synonyms and other info pulled from PATO in the bcodmont Quantifier component ontology

Reminder: Date/Time still do not exist in the ontology. These need to be handled.

For new term requests, please provide the following information:

Preferred term label

time zone

Synonyms

see bco-dmo.org/parameter/1012

Textual definition

from http://purl.obolibrary.org/obo/NCIT_C80453

A geographic region throughout which the same standard time is used.

Suggested parent term

Operational > Geographic area

Attribution

0000-0003-1023-6239