adding molecularEntity

[lzehl]

@tgbugs & @UlrikeS91 I'm surprised that no one requested that yet... we postponed this for a while. do you agree adding the schema and at least some instances?

[@UlrikeS91 did you prepare something for this already? I have the feeling you did... if so, feel free to forward, I can take over if you want]

[UlrikeS91]

Yes, I have some first instances for a molecularEntity terminology ☺️ I have a list that includes more than just those, so it's not smart to link it here. But we can discuss the list offline and I can make a PR with what we landed on/want to include (which can be up for feedback from the broader community afterwards instead).

Sounds good?

[tgbugs]

I'm guessing the domain is CHEBI + protein ontology/uniprot, so small molecules and proteins? Would this also cover engineered proteins such as eGFP, RFP, etc. which might have certain metadata templates about excitation frequencies or similar?

[UlrikeS91]

@tgbugs, here is an excerpt from the list. "Keywords from EBRAINS KG" are terms that have been stated as keywords in KG v2, then I did a rough "categorization" stating a potential terminology the term could fit in (here you only got the terms that could have something to do with molecular entities), "openMINDS (potential) name" states the (re)curate name of the term (work in progress, which is why several of them are still empty), "InterLex" states the InterLex IRI (if I could find one) and "preferred ontology ID" states either the IRI that has been stated as preferred in InterLex or, if I couldn't find it in InterLex, another ontology. When a term wasn't included in InterLex, my first "go-to" was CHEBI. In some cases, I also used the CHEBI as preferred ID even though InterLex stated something else as preferred (e.g. for chemical agents like isoflurane or DAB). A few also point to the protein ontology (e.g. Neuroligin 3) but I think those are mostly cases where the protein ontology was listed in InterLex.

eGFP, RFP and such haven't been used as keywords in the KG. Closest to those are probably terms like "Alexa Fluor 594" or "FluorRuby", which I would include in the molecularEntity terminology for openMINDS. So, I would probably add terms like eGF/RFP/etc. as well. The original idea for this terminology was to not restrict it too much and collect anything that loosely related to it, and rather later on split it up into several sub-terminologies (with stricter definitions).

keyword from EBRAINS KG	categorization	openMINDS (potential) name	InterLex	preferred ontology ID
ABetaX-40	MolecularEntity	Beta-Amyloid 40	http://uri.interlex.org/ilx_0101246	http://uri.neuinfo.org/nif/nifstd/nlx_13181
adenosine receptor A1	MolecularEntity	adenosine A1 receptor	http://uri.interlex.org/ilx_0100146	http://uri.neuinfo.org/nif/nifstd/nifext_5717
adenosine receptor A2A	MolecularEntity	adenosine A2A receptor	http://uri.interlex.org/ilx_0100148	http://uri.neuinfo.org/nif/nifstd/nifext_7727
Alexa Fluor 594	MolecularEntity	Alexa Fluor 594	null	http://purl.obolibrary.org/obo/CHEBI_51248
Anterograde Tracer	MolecularEntity	anterograde tracer	null	http://purl.obolibrary.org/obo/NLXMOL_1012002
anterograde tracer	MolecularEntity	anterograde tracer	null	http://purl.obolibrary.org/obo/NLXMOL_1012002
BDA	MolecularEntity	biotinylated dextran amine	http://uri.interlex.org/ilx_0450726	http://id.nlm.nih.gov/mesh/2018/M0205506
biomarkers	MolecularEntity	biomarker	http://uri.interlex.org/ilx_0101294	http://uri.neuinfo.org/nif/nifstd/nlx_mol_20090517
Biotinylated dextran amine	MolecularEntity	biotinylated dextran amine	http://uri.interlex.org/ilx_0450726	http://id.nlm.nih.gov/mesh/2018/M0205506
C-fos	MolecularEntity	c-FOS	null	null
Ca2+/calmodulin-dependent protein kinase II promoter	MolecularEntity	calcium calmodulin protein kinase II promoter	null	null
	MolecularEntity	calcium calmodulin protein kinase II	http://uri.interlex.org/ilx_0101561	http://purl.obolibrary.org/obo/PR_000003197
Calbindin	MolecularEntity	calbindin	http://uri.interlex.org/ilx_0101551	http://uri.neuinfo.org/nif/nifstd/nlx_mol_1006006
Calretinin	MolecularEntity	calretinin	http://uri.interlex.org/ilx_0101602	http://uri.neuinfo.org/nif/nifstd/nifext_5717
Camk2a	MolecularEntity	calcium calmodulin protein kinase II alpha chain	null	http://purl.obolibrary.org/obo/PR_000003199
Chemical markers	MolecularEntity	chemical marker	null	null
cyclic AMP	MolecularEntity	cyclic adenosine monophosphate	http://uri.interlex.org/ilx_0100318	http://purl.obolibrary.org/obo/CHEBI_17489
DAB	MolecularEntity	DAB	http://uri.interlex.org/ilx_0482636	http://purl.obolibrary.org/obo/CHEBI_90994
Dopamine D1 receptor	MolecularEntity	D1 dopamine receptor	http://uri.interlex.org/ilx_0102774	http://uri.neuinfo.org/nif/nifstd/nifext_5845
Dopamine D2 receptor	MolecularEntity	D2 dopamine receptor	http://uri.interlex.org/ilx_0102775	http://uri.neuinfo.org/nif/nifstd/nifext_5833
Fluorescent microspheres	MolecularEntity	fluorescent microspheres	null	null
Fluoro-gold	MolecularEntity	Fluoro-Gold	http://uri.interlex.org/ilx_0104323	http://uri.neuinfo.org/nif/nifstd/nlx_30125
FluoroEmerald	MolecularEntity	Fluoro-Emerald	null	null
FluoroRuby	MolecularEntity	Fluoro-Ruby	http://uri.interlex.org/ilx_0104322	http://uri.neuinfo.org/nif/nifstd/nlx_65982
GABA receptor	MolecularEntity	GABA receptor	http://uri.interlex.org/ilx_0104502	http://uri.neuinfo.org/nif/nifstd/nlx_mol_1006001
GABAA receptor	MolecularEntity	GABA-A receptor	null	null
GABAB receptor	MolecularEntity	GABA-B receptor	http://uri.interlex.org/ilx_0104503	http://uri.neuinfo.org/nif/nifstd/nlx_mol_090801
GLT1	MolecularEntity	glutamate transporter 1	null	null
Glutamate transporter	MolecularEntity	glutamate transporter	http://uri.interlex.org/ilx_0104678	http://uri.neuinfo.org/nif/nifstd/sao1399894198
Glycine transporter type 2	MolecularEntity	glycine transporter 2	null	null
Growth factor	MolecularEntity	growth factor	http://uri.interlex.org/ilx_0104801	http://uri.neuinfo.org/nif/nifstd/sao1671627152
Intrabodies	MolecularEntity	intrabody	null	null
	MolecularEntity	ionotropic glutamate receptor	http://uri.interlex.org/ilx_0105706	http://uri.neuinfo.org/nif/nifstd/nlx_mol_20090501
ionotropic glutamate AMPA receptor	MolecularEntity	AMPA receptor	http://uri.interlex.org/ilx_0100559	http://uri.neuinfo.org/nif/nifstd/nifext_5251
ionotropic glutamate kainate receptor	MolecularEntity	kainate receptor	http://uri.interlex.org/ilx_0105822	http://uri.neuinfo.org/nif/nifstd/nifext_5252
ionotropic glutamate NMDA receptor	MolecularEntity	NMDA receptor	http://uri.interlex.org/ilx_0107622	http://uri.neuinfo.org/nif/nifstd/nifext_5250
IPEROXO	MolecularEntity	iperoxo	http://uri.interlex.org/ilx_0630403	http://id.nlm.nih.gov/mesh/2018/M000598130
Isoflurane	MolecularEntity	isoflurane	http://uri.interlex.org/ilx_0105740	http://purl.obolibrary.org/obo/CHEBI_6015
JNK MAP kinase scaffold protein 2	MolecularEntity	JNK MAP kinase scaffold protein 2	null	http://purl.obolibrary.org/obo/PR_000010161
Kallikrein related-peptidase 8	MolecularEntity	kallikrein-related peptidase 8	null	http://purl.obolibrary.org/obo/PR_000009614
Ketamine	MolecularEntity	ketamine	http://uri.interlex.org/ilx_0105850	https://www.drugbank.ca/drugs/DB01221
M2 receptor	MolecularEntity	muscarinic acetylcholine receptor 2	http://uri.interlex.org/ilx_0106430	http://uri.neuinfo.org/nif/nifstd/nifext_7946
Medetomidine	MolecularEntity	medetomidine	http://uri.interlex.org/ilx_0488544	http://purl.obolibrary.org/obo/CHEBI_48552
muscarinic acetylcholine receptor M1	MolecularEntity	muscarinic acetylcholine receptor 1	http://uri.interlex.org/ilx_0106429	http://uri.neuinfo.org/nif/nifstd/nifext_7348
muscarinic acetylcholine receptor M2	MolecularEntity	muscarinic acetylcholine receptor 2	http://uri.interlex.org/ilx_0106430	http://uri.neuinfo.org/nif/nifstd/nifext_7946
muscarinic acetylcholine receptor M3	MolecularEntity	muscarinic acetylcholine receptor 3	http://uri.interlex.org/ilx_0106431	http://uri.neuinfo.org/nif/nifstd/nifext_6131
NeuN	MolecularEntity	neuronal nuclear antigen	http://uri.interlex.org/ilx_0107517	http://uri.neuinfo.org/nif/nifstd/nlx_152221
Neurobiotin	MolecularEntity	neurobiotin	http://uri.interlex.org/ilx_0107453	http://uri.neuinfo.org/nif/nifstd/nlx_157299
Neuroligin 3	MolecularEntity	neuroligin-3	http://uri.interlex.org/ilx_0107485	http://purl.obolibrary.org/obo/PR_000011256
Neuropsin promoter	MolecularEntity	kallikrein-related peptidase 8 promoter	null	null
Neurotransporter	MolecularEntity	neurotransmitter transporter	null	null
Neurotrophic factor	MolecularEntity	neurotrophic factor	null	null
nicotinic acetylcholine alpha4beta2 receptor	MolecularEntity	nicotinic receptor alpha4beta2	http://uri.interlex.org/ilx_0597802	http://id.nlm.nih.gov/mesh/2018/M0356600
Nop	MolecularEntity	kallikrein-related peptidase 8	null	http://purl.obolibrary.org/obo/PR_000009614
noradrenergic receptor alpha1	MolecularEntity	alpha-1 adrenergic receptor	null	null
noradrenergic receptor alpha2h	MolecularEntity	alpha-2H adrenergic receptor	null	null
PAI (Phthalimide-Azo-Iperoxo)	MolecularEntity	Phthalimide-Azo-Iperoxo	null	null
Parvalbumin	MolecularEntity	parvalbumin	http://uri.interlex.org/ilx_0108558	http://uri.neuinfo.org/nif/nifstd/nifext_6
Pcp2	MolecularEntity
Phaseolus vulgaris leucoagglutinin	MolecularEntity
Phosphodiesterases	MolecularEntity
Pituitary homeobox 3 promoter	MolecularEntity
Pitx3	MolecularEntity
Prion protein promoter	MolecularEntity
Prnp	MolecularEntity
Protein Kinase A	MolecularEntity
Prss19	MolecularEntity
Purkinje cell protein 2 promoter	MolecularEntity
Retrograde Tracer	MolecularEntity
serotonin receptor 5-HT1A	MolecularEntity
serotonin receptor 5-HT2	MolecularEntity
Serum biomarkers from cord blood at birth	MolecularEntity
Serum biomarkers from mother during pregnancy	MolecularEntity
Somatostatin	MolecularEntity
Tetracycline transactivator	MolecularEntity
Tetracycline transactivator protein	MolecularEntity
tTA	MolecularEntity
Vasoactive intestinal peptide	MolecularEntity
VGLUT3	MolecularEntity	vesicular glutamate transporter 3	null	null
Wheat germ agglutinin-horseradish peroxidase	MolecularEntity
X-gal	MolecularEntity
3H-Oxotremorine autoradiography	MolecularEntity
Camk2a-tTA	MolecularEntity ORStrain
CaMKII-tTA	MolecularEntity ORStrain
EC-tTA	MolecularEntity ORStrain
Klk8-tTA	MolecularEntity ORStrain
Nop-tTA	MolecularEntity ORStrain
Pcp2-tTA	MolecularEntity ORStrain
Pitx3-tTA	MolecularEntity ORStrain
Prnp-tTA	MolecularEntity ORStrain
tTA-EC	MolecularEntity ORStrain
Fast blue	MolecularEntity?
Green beads	MolecularEntity?
Red beads	MolecularEntity?
Tet-lacZ reporter	MolecularEntity?

[tgbugs]

A quick look suggest that most of these are correctly classified as molecular entities, however there are quite a few, such as retrograde tracer, neuropsin promoter, and others that are more correctly roles that a molecular entity can play.

[lzehl]

@tgbugs I will prepare a PR with a couple of molecular entities. Could you have a look at it once I upload the respective instances and comment on the ones that are critical (should be listed in another terminology)?

[lzehl]

this one was done in a first PR #85