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Home Page: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-015-0005-5
License: Other
The eNanoMapper ontology
Home Page: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-015-0005-5
License: Other
we need to import the serum types from the cell culture ontology (CCONT) -- they are classified beneath 'mixture' in CCONT along with a class called 'Medium condition' which should be excluded as it includes too many vaguely grouped together things to be useful.
http://purl.obolibrary.org/obo/CHEBI_83159 copper(II) oxide nanoparticle
move from http://purl.obolibrary.org/obo/CHEBI_52855 (inorganic nanoparticle)
to
http://purl.bioontology.org/ontology/npo#NPO_1541 (metal oxide nanoparticle)
e.g. cell viability: synonym (I don't think a subclass is needed for that issue): PI assay, BJ assay, Alamar blue assay, LDH assay
So people searching for e.g. "Hoechst assay" will get the results for any "apoptosis assay"
Could someone (@fehrhart @lrieswijk ?) please help with suggesting the correct ontology (BAO?) entry for the following two assays:
Both used in doi:10.1371/journal.pone.0127174
biopersistence & persistence as synonyms for bioavailability
Could you point to eNanoMapper ontology entries to represent experimental protocol , or type of assay ; e.g. similar to
Hi
You may wish to incorporate (parts of) the Exposure Ontology (EXO), which is available from BioPortal?
For example, as far as I can see, the eNanoMapper ontology does not currently have a class for the important concept of "exposure medium" (e.g. the liquid mixture via which nanomaterials are exposed to the cells in in vitro assays).
The Exposure Ontology has was seems to be a suitable class for this: http://purl.obolibrary.org/obo/ExO_0000083
HTH
Richard
In the following entry: http://aber-owl.net/ontology/ENM#!http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0000015
there is a typo: "a set of instructions, methodology, operations, required reagents, instruments to carrie out experiments".
When releasing the ontology, will there be formal version release numbers e.g. for the "alpha" version currently on BioPortal (http://bioportal.bioontology.org/ontologies/ENM)? (Please excuse me if this point has already been addressed and I have not noticed!) This would facilitate citing and referencing within an ISA-TAB (or ISA-TAB-Nano) Investigation file.
(I may be digressing, but I would point out that - for the purpose of constructing ISA-TAB or ISA-TAB-Nano Investigation files - I would personally interpret the submission number after ".../submissions/..." in the OWL file download link [e.g. http://data.bioontology.org/ontologies/ENM/submissions/1/download?apikey=..... etc.] as the version number if the ontology is available from BioPortal as this seems consistent with the ISA-TAB example files: http://isatab.sourceforge.net/examples.html )
Hi all, (@JKChang2015 @G-Owen @lrieswijk @vedina @fehrhart)
we now have a steady flow of ontology requests, but not enough people making patches. I think we should have a number of very technical, hands-on, online hackathon meetings with the WP2 and WP3 people (probably also WP4/WP5 as use case owners) for internal teaching of making patches. We should not longer await what the other is doing, but get our hands dirty, make mistakes, confront upstream, and learn.
I rather have this meeting inclusive (the more people, the merrier) and more than happy with external people joining, but it seems we need internal education in the first one/two meetings.
The purpose would be educate ourselves, identify road blocks, find best practices, etc, but secondly and importantly, make sure we grow our ontology (and upstream ones). The rate delimiting factor no longer seems to be identifying the right upstream ontologies, but to extend them in a sustainable way.
Please comment here if you like to join, and then we can identify a weekly telcon time. @G-Owen, whom else should we invite from with ENM that we need to join from the start? It should be technical people that will actually and personally make patches.
Egon
e.g. Sigma Aldrich -- and the different locations of the manufacturers.
Are these already in a database or ontology? -- need a unified vocabulary.
http://purl.obolibrary.org/obo/CHEBI_52733 dieuropium trioxide nanoparticle
move from http://purl.obolibrary.org/obo/CHEBI_52855 (inorganic nanoparticle)
to
http://purl.bioontology.org/ontology/npo#NPO_1541 (metal oxide nanoparticle)
investigate for inclusion
@fehrhart , @lrieswijk
While trying to serialize enanomapper database study content using BAO , I've noticed the PubChem assay annotation uses SIO to define properties as has-value
, has-units
, etc. It seems also SIO has properties defined which can be used to describe value-less-than-something
, etc. which will be very helpful.
Do we already have such terms in enanomapper ontology, and if not, should we consider adding ones from SIO?
Examples:
Related issue enanomapper/data.enanomapper.net#9
http://purl.obolibrary.org/obo/CHEBI_50831 platinum nanoparticle
move from
http://purl.obolibrary.org/obo/CHEBI_52855 inorganic nanoparticle
to
http://purl.bioontology.org/ontology/npo#NPO_1384 metal nanoparticle
http://purl.obolibrary.org/obo/CHEBI_50824 hematite nanoparticle
and
http://purl.bioontology.org/ontology/npo#NPO_1550 Iron(III)oxide nanoparticle
they are identical (Fe2O3)
triclinic, etc, -> all of them, not a subset.
Related, anatase/rutile are different; the first is a mixture of crystallinity types for TiO2.
http://purl.bioontology.org/ontology/npo#NPO_1548 iron(II,III) oxide
and
http://purl.obolibrary.org/obo/CHEBI_50823 magnetite
they are identical (both Fe3O4 nanoparticles)
The following two metadata fields are now empty:
PUBLICATIONS PAGE
DOCUMENTATION PAGE
Please help mapping these terms to ontology entries - could be one or more annotation per term.
aids used to disperse/sonification
aids used to disperse/stirring
aids used to disperse/vortexing
cell culture conditions - medium
cell culture conditions - serum
cell culture conditions - serum concentration in growth medium
cell culture conditions - serum concentration in treatment medium
cell line/type - full name
cell line/type - short name
cell line/type - supplier
dispersion agent
dispersion protocol
concentration
time point
replicate
From a private email:
It seems that http://purl.enanomapper.org/onto/ENM_0000060 (NOEC, no
observed effect concentration), is unsatisfiable when the ontology is
classified. As a result, it currently shows up as a subclass of every
class in ENM (since it becomes equivalent to owl:Nothing), which is
probably not intended. It also is messing up [the] display of that
class, which is a bug we'll fix soon (we'll show a list of all
unsatisfiable classes instead and never include them in the treeview).
Please check
<owl:Class rdf:about="&resource;NM_001005">
<rdfs:label>particle size descriptor</rdfs:label>
<rdfs:subClassOf rdf:resource="&resource;NM_000005"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;IAO_0000136"/>
<owl:someValuesFrom rdf:resource="&resource;NM_000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<description>Describes the particle size. The actual approach to describes it is
undefined at this level.</description>
</owl:Class>
<owl:Class rdf:about="&resource;NM_001005">
<rdfs:label>zetapotential descriptor</rdfs:label>
<rdfs:subClassOf rdf:resource="&resource;NM_000006"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;IAO_0000136"/>
<owl:someValuesFrom rdf:resource="&resource;NM_000001"/>
</owl:Restriction>
</rdfs:subClassOf>
<description>Describes the zeta potential of the nanomaterial. The potential
may be experimental, predicited, or originating from a read-across approach.</description>
</owl:Class>
we need to add cell lines e.g. HUVEC. Need to determine which is the best ontology to use for this (candidates: Cell Line Ontology; BRENDA tissue ontology) -- and whether to import in full or to import only as-needed (depending on size of the ontology)
... favour the 'endpoint' parent as this is the way toxicologists think of toxicological categories
(but not all the subclasses obviously as that is the root term :-))
At this moment the owl:import approach was shown to not work well. It results in duplication of terms in various ways, for example, same URI with mupltiple labels; same term with different URIs. To address this we need a custom, more general approach to import (parts of) 3rd party ontologies.
Hi
How is the issue of nanomaterial functionality (from an industry/product point of view) addressed in the ontology?
I checked for terms like "functionality" and specific types of functionality, such as antibacterial, but I couldn´t find that.
Is there an existing functionality ontology that could serve as the basis for a nano-specific functionality ontology? Would the chEBI ontology be a good basis? I found others that could be relevant too (e.g. PATO and different medical ontologies), but which one is the best may need to be discussed, or is this discussion already taking place?
Penny
investigate the rest of the ontology for inclusion?
I noticed that a lot of new terms coming from a particular project are best reflected in NCIT. So it would be great if this ontology could be added to the eNanoMapper Ontology
Apologies, not really an ENM ontology issue, rather BAO.
It is confusing to find two entries for biological process in BAO : biological process
BAO_0000264 and biological_process
GO_0008150. Does anybody has an insight on this (and which entry is recommended)?
investigate how much to include and overlap with other ontologies
Some are missing in ENM (or I couldn't find)
Bioassay:
Biologic "material" to test nanoparticles with:
Species
Rat, mice, human, zebrafish
Cell culture
primary, cell lines on demand
Exposure conditions:
Single exposure
Time, Dose, application route (oral, dermal, inhalation)
Repeated dose experiment
Time, Dose, application route (oral, dermal, inhalation)
Test assays:
in vitro
e.g. life-dead assay: PI assay, Hoechst assay, LDH assay
in vivo (ex vivo)
clinical trials (?)
... into subclass descriptors for values calculated with a specific Mopac version. I found PM6 values between 2009 and 2012 to differ, and Mopac2012 also has a new PM7 method.
def: see wikipedia
Is there a link in the ENM ontology, allowing to represent the zinc oxide nanoparticle
and the zinc oxide
CHEBI_36560 are related?
I'm looking for automatic means to retrieve this linking information and support user friendly search, as people will be usually searching for ZnO
and not necessary for ZnO nanoparticle
, while expecting the nanoparticles to show up.
Add a section about application of nanoparticle, e.g. commercial use (sunscreen), potential use, e.g. drug delivery or scientific interest (antibiotic)
definition: the date beyond which a commodity is no longer regarded as fit for use.
synonyms: expiration date; shelf life
http://purl.obolibrary.org/obo/BFO_0000001
Does not have a description.
http://purl.obolibrary.org/obo/CHEBI_51050 titanium dioxide nanoparticle
move from
http://purl.obolibrary.org/obo/CHEBI_52855 (inorganic nanoparticle)
to
http://purl.bioontology.org/ontology/npo#NPO_1541 (metal oxide nanoparticle)
We stumbled across some URIs that need to be incorporated in the ENM ontology. Mentioned below are the ontology source and then the respective URIs.
ADW:
Measurement_units
BAO:
BAO_0000520
CRISP:
3091-4941
CSEO
Exposure_Concentration
EFO:
EFO_0001444
EFO_0005067
GO:
GO_0009293
HUPSON:
hupson:SCAIVPH_00000886
hupson:SCAIVPH_00000190
hupson:SCAIVPH_00000392
IAO:
IAO_0000301
NCIT:
C119826
C17941
C25169
C25284
C25365
C25492
C25572
C25625
C25681
C38389
C42651
C42721
C43531
C44473
C45805
C46003
C50400
C54166
C61299
C61412
C68553
C68806
C71477
C80514
C83039
C88214
C16866
C18189
C25209
C25212
C25246
C25247
C25474
C25666
C33177
C41130
C42614
C42680
C42709
C43530
C45518
C48041
C48937
C49507
C52478
C53321
C62352
C70766
C90446
C25474
NIF:
nlx_res_090901
NPO:
NPO_1517
NPO_1167
NPO_1344
NPO_1345
NPO_1364
NPO_1573
NPO_1812
NPO_1818
NPO_1853
OBI:
OBI_0000272
OBI_0000835
OBI_0000984
OBI_0001152
OBI_0001185
OBI_0000018
OBI_0000031
OBI_0001876
OBI_0100026
PATO:
PATO_0000011
PATO_0000068
PATO_0000165
PATO_0002175
PATO_0000117
PATO_0000052
PATO_0000122
PATO_0000146
PATO_0000918
PATO_0000921
PATO_0001334
PATO_0001555
SNOMEDCT:
4601000
46595003
246093002
261586004
277046005
304889007
I'm looking for ontology annotation of
Phorbol 12-myristate 13-acetate transformed THP.1 cells (Human monocyte derived macrophages)
cc @lrieswijk @egonw
These items are not yet covered by any ontology:
copper nanoparticle
zirconium dioxide nanoparticle
fullerenol nanoparticle
polyethylenglycol nanoparticle
germanium nanoparticle
molybdenum trioxide nanoparticle
aluminum nanoparticle
cadmium(II) oxide nanoparticle
Manganese (IV) dioxide nanoparticle
tungsten nanoparticle
tricalcium phosphate nanoparticle
Some details and information (sheet 3):
https://docs.google.com/spreadsheets/d/1CeAjmJFqjrLD14GNphjaCSUlaTaSwHfV91MA4e5oi4M/edit?usp=sharing
The scenario I am thinking about would be assigning an entry for the ISA-TAB-Nano Material file "Material Chemical Name" field, but this could be a more generally applicable concern.
There appears a need for suitable, generic chemical names (based upona quick search of both eNM and CHEBI via BioPortal) e.g. "titanium dioxide nanoparticle" appears but not a generic "titanium dioxide". My understanding is that, according to some definitions at least, "nanoparticle" means all three dimensions are in the nanoscale range so this might not be most appropriate for a "titanium dioxide" nanomaterial of some other form. The ChEBI definition of "titanium dioxide" is perhaps problematic due to the suggestion that it is a molecular entity associated with the synonym "O=[Ti]=O", whereas nanomaterial TiO2 is more likely a crystal structure (Ti---O---Ti etc.) which is not based on such discrete molecular entities. Are there any possible ways to address this? Other ontology imports? De novo creation?
http://purl.obolibrary.org/obo/CHEBI_52853 palladium nanoparticle
move from
http://purl.obolibrary.org/obo/CHEBI_52855 inorganic nanoparticle
to
http://purl.bioontology.org/ontology/npo#NPO_1384 metal nanoparticle
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