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Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/6
Reported by Caty Chung
cell line
This is confusing to me. Please check if this is how it should be.
In BioPortal I search "cell line". I see - screenshot.
http://www.bioassayontology.org/bao#BAO_0002931
http://purl.obolibrary.org/obo/CLO_0000001
I see a lot of repeating stuff in BioPortal, which I do not see the same way in
Protege. Looks like things with "="
When we extracted both from BAO 2.0, we see that they seem equivalent (refer to
the following records)
CLO_0000001 'cell line cell' topBAOClass->'assay biology component'->'cell line
cell'
BAO_0002931 'cell line cell' topBAOClass->'assay biology component'->'cell line
cell'
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 6:17
Attachments:
Hi,
there several terms are not addressable by using the following URLs. Pl
http://www.bioassayontology.org/bao#BAO_0001094
http://www.bioassayontology.org/bao#BAO_0001067
http://www.bioassayontology.org/bao#BAO_0000540
After digging it, I found they are in this file, bao_complete_merged.owl, but not in bao_complete.owl.
But the default url point to bao_complete.owl. Is it a bug?
Best,
Leon
http://www.bioassayontology.org/bao#BAO_0003109
Add a kit after KINOMEScan.
Discussed on MIAMI ontology meeting (3-4-2016)
Hello. I can't find the term "high throughput screening (HTS)" in the ontology and wonder if you would be able to add this term? As it is very common term used by early drug discovery scientists, it would be useful to have it in the ontology as a term rather than a definition or synonym.
Tx, Anneli
There are labels with a suffix _bao in the tree, the "_bao" suffix needs removed.
UCSF uses "equilibrium" as an additional option for assay state (vs end point or kinetic). This is not necessarily the best place for it, but the inherent definition for our use case does not match the equilibrium dialysis already present under bioassay.
The system being at equilibrium is required for some binding assays (including, but not limited to, SPR, fluorescence polarization, radioligand).
Some of the references sent to me by my staff:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000649/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993736/
move it to its correct location
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/3
From Linda:
I agree with the Calcium redistribution, but cAMP and cGMP is formed in
response to GPCR signaling. IP1 seems to be a metabolite formed during IP3
breakdown. Second messenger assay might therefore be better and cAMP regulation
or cAMP signaling assay?
I find it a bit confusing with the ‘mode of action’ label on the class that
rather, as I understand it, describes the mechanism of action. I am also a
little puzzled by the ‘second messenger assay’ and the’ second messenger
redistribution assay’ class that seems to be equivalent. Also, the subclasses
‘cAMP redistribution assay’ and ‘IP1 redistribution assay’ suggest that
there is a redistribution of these second messengers.
What is the reason for using these labels?
From Uma:
my suggestion is to remove the equivalency between the cAMP redistribution and
signaling assays. See below an e.g. of a cAMP redistribution assay.
reference:
Science. 2010 Mar 26;327(5973):1653-7. doi: 10.1126/science.1185988. Epub 2010
Feb 25.
Beta2-adrenergic receptor redistribution in heart failure changes cAMP
compartmentation.
Nikolaev VO1, Moshkov A, Lyon AR, Miragoli M, Novak P, Paur H, Lohse MJ,
Korchev YE, Harding SE, Gorelik J.
Abstract
The beta1- and beta2-adrenergic receptors (betaARs) on the surface of
cardiomyocytes mediate distinct effects on cardiac function and the development
of heart failure by regulating production of the second messenger cyclic
adenosine monophosphate (cAMP). The spatial localization in cardiomyocytes of
these betaARs, which are coupled to heterotrimeric guanine nucleotide-binding
proteins (G proteins), and the functional implications of their localization
have been unclear. We combined nanoscale live-cell scanning ion conductance and
fluorescence resonance energy transfer microscopy techniques and found that, in
cardiomyocytes from healthy adult rats and mice, spatially confined
beta2AR-induced cAMP signals are localized exclusively to the deep transverse
tubules, whereas functional beta1ARs are distributed across the entire cell
surface. In cardiomyocytes derived from a rat model of chronic heart failure,
beta2ARs were redistributed from the transverse tubules to the cell crest,
which led to diffuse receptor-mediated cAMP signaling. Thus, the redistribution
of beta(2)ARs in heart failure changes compartmentation of cAMP and might
contribute to the failing myocardial phenotype.
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 5:47
Add cell property (cell state) to BAO:
https://bioportal.bioontology.org/ontologies/EFO?p=classes&conceptid=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0002954
Include children: differentiated, pluripotent, or primary cell
Not sure, but I do not seem able to find it in the repository, and the description for BAO_0002162
seems missing.
There are duplicated Biological_process terms in BAO.
The following defines GO_0008150 is equivalent term of BAO_0000264.
We should directly use GO term instead of create another BAO equivalent term.
<!-- http://purl.obolibrary.org/obo/GO_0008150 -->
<rdf:Description rdf:about="&obo;GO_0008150">
<owl:equivalentClass rdf:resource="http://www.bioassayontology.org/bao#BAO_0000264"/>
<rdfs:subClassOf rdf:resource="http://www.bioassayontology.org/bao#BAO_0003114"/>
<obo:IAO_0000412 rdf:resource="&obo;go.owl"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_aspergillus"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_candida"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_generic"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_metagenomics"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_pir"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_plant"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_pombe"/>
<oboInOwl:inSubset rdf:resource="&obo;go#goslim_yeast"/>
<oboInOwl:inSubset rdf:resource="&obo;go#gosubset_prok"/>
</rdf:Description>
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/8
Dear Caty, Stephan,
with some months delay, please find attached the end points I encoded in BAO
terms for some of my Open PHACTS work. I have been very busy with too many
things, and I hope you can accept my apologies for the delay. One of the
reasons was the start of the eNanoMapper project where we will use BAO too.
Janna Hastings is also involved in this new EU project.
I also like you to know that I have a PhD student now working on
ontology-encoding some of the nanotox data for eNanoMapper. He is defining
missing assays too.
Is there a block of BAO_xxxx codes that can be reserved for things we do?
Egon
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Egon Willighagen added a comment - 19/May/14 8:54 AM
Mmm... this Atlassian doesn't allow attachments? OK: here it is (Stephan, some
you already added...):
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix qudt: <http://qudt.org/schema/qudt#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix ops: <http://www.openphacts.org/assays/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix bao: <http://www.bioassayontology.org/bao#> .
ops:pKi
rdfs:subClassOf bao:BAO_0000192 ;
rdfs:label "pKi"^^xsd:string ;
obo:IAO_0000115 "pKi is the -log Ki, where Ki is the equilibrium inhibitor
dissociation constant."@en ;
obo:IAO_0000118 "-log Ki"^^xsd:string .
ops:A2
rdfs:subClassOf bao:BAO_0002162 ;
rdfs:label "A2"^^xsd:string ;
obo:IAO_0000115 "The molar concentration of antagonist which requires the
agonist concentration to be doubled in order to achieve the original re
sponse."@en .
bao:BAO_0003038
rdfs:subClassOf ops:A2 .
ops:pMIC
rdfs:subClassOf bao:BAO_0002146 ;
rdfs:label "pMIC"^^xsd:string ;
obo:IAO_0000115 "pMIC is the -log MIC, where MIC is the lowest concentration of
an inhibitor (antimicrobial agent) required to inhibit the growth
of a microorganism."@en ;
obo:IAO_0000118 "-log MIC"^^xsd:string .
ops:pKd
rdfs:subClassOf bao:BAO_0000034 ;
rdfs:label "pKd"^^xsd:string ;
obo:IAO_0000115 "pKd is the -log Kd, where Kd is the equilibrium dissociation
constant for a drug."@en ;
obo:IAO_0000118 "-log Kd"^^xsd:string .
ops:IC20
rdfs:subClassOf bao:BAO_0002162 ;
rdfs:label "IC20"^^xsd:string ;
obo:IAO_0000115 "The effective concentration of an inhibitor, which produces
20% of the maximum possible response for that inhibitor."@en .
ops:IC25
rdfs:subClassOf bao:BAO_0002162 ;
rdfs:label "IC25"^^xsd:string ;
obo:IAO_0000115 "The effective concentration of an inhibitor, which produces
25% of the maximum possible response for that inhibitor."@en .
ops:IC30
rdfs:subClassOf bao:BAO_0002162 ;
rdfs:label "IC30"^^xsd:string ;
obo:IAO_0000115 "The effective concentration of an inhibitor, which produces
30% of the maximum possible response for that inhibitor."@en .
ops:pIC20
rdfs:subClassOf ops:IC20 ;
rdfs:label "pIC20"^^xsd:string ;
obo:IAO_0000115 "pIC20 is the -log IC20, where IC20 is the effective
concentration of an inhibitor, which produces 20% of the maximum possible re
sponse for that inhibitor."@en .
obo:IAO_0000118 "-log IC20"^^xsd:string .
ops:pIC25
rdfs:subClassOf ops:IC25 ;
rdfs:label "pIC25"^^xsd:string ;
obo:IAO_0000115 "pIC25 is the -log IC25, where IC25 is the effective
concentration of an inhibitor, which produces 20% of the maximum possible re
sponse for that inhibitor."@en .
obo:IAO_0000118 "-log IC25"^^xsd:string .
ops:pIC30
rdfs:subClassOf ops:IC30 ;
rdfs:label "pIC30"^^xsd:string ;
obo:IAO_0000115 "pIC30 is the -log IC30, where IC30 is the effective
concentration of an inhibitor, which produces 20% of the maximum possible re
sponse for that inhibitor."@en .
obo:IAO_0000118 "-log IC30"^^xsd:string .
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 7:24
Per discussions a new file is created and new terms created via the discussions need added.
Hi,
I tried loading the BAO owl file using ROBOT, but when I import the vocab via the URL http://purl.obolibrary.org/obo/agro.owl it is unable to find one of the imported OWL files - http://www.bioassayontology.org/bao/external/BAO_NCIT_import.owl
I had a look at this page and I get an HTTP 404 error.
Cheers,
Mark
To improve the ontology and make it more usable you could include the negative logarithm to base 10 of the equilibrium dissociation constant, K in molar concentration units - pK. This can be used in combination with subscripts for regular equilibrium dissociation constants. Details and Notes can be found at:
http://www.guidetopharmacology.org/pdfs/termsAndSymbols.pdf
Thank you very much!
When I fetched subject ontology from http://www.bioassayontology.org/bao/bao_complete.owl and tried loading it using Apache Jena, I got a RiotException that the file had an invalid format:
[line: 248, col: 10] {E202} Expecting XML start or end element(s). String data "\" not allowed. Maybe a striping error.
At line 248, there is a stray "\" in the file. Deleting this allowed the file to load.
I ran into this problem after upgrading the eNanoMapper Slimmer
tool to OWLAPI 5.1.1 with loading of http://www.bioassayontology.org/bao/bao_complete.owl
, but can confirm it with the latest Protege too. The phenotype is this error message (for both):
Ontology already exists. OntologyID(OntologyIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>) VersionIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>))
I ran into this problem for the CHEMINF
ontology too, an discovered a circular dependency. When I remove that circular dep, then both tools were able to load the ontology. For BAO
I notice the same problem, and suspect this to be the reason here too, why the two tools cannot load ontology: bao_complete.owl
imports bao_core.owl
and bao-core.owl
imports bao_complete.owl
:
<owl:Ontology rdf:about="http://www.bioassayontology.org/bao/bao_core.owl">
<owl:versionIRI rdf:resource="http://www.bioassayontology.org/bao/bao_core.owl"/>
<owl:imports rdf:resource="http://www.bioassayontology.org/bao/bao_external.owl"/>
<owl:imports rdf:resource="http://www.bioassayontology.org/bao/bao_complete.owl"/>
add the axiom to the definition of term "assay"
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/9
Reported by Linda Zander Balderud on 22/Dec/14 10:03 AM
A list of questions and suggestions that are either new or have been discussed
before but are not yet changed in the ontology.
1. Does ’ratio’ belong to ’unit of measurement’ or should it be an
endpoint (see my comment on phenotypic endpoint annotation)?
2. Addition of ‘Secretory alkaline phosphatase reporter gene assay’ and
‘ligase activity assay’ bioassay.
3. Name change from cAMP, cGMP and IP1 redistribition assay to cAMP, cGMP and
IP1 second messenger
4. Assay design method and Physical detection method of HPLC assays?
5. In a knockdown gene expression modulation method, which property should I
use do define the targeted gene?
6. Is there a way to annotate protocol version number, I did see it in a
previous version of BAO.
7. Property to define Image analysis software
8. Property to define emission filter
9. Will dispensing instrument be part of the ontology? I once put together of
instruments we use within AZ as requested from Uma but it seems not to be in
BAO2.0.
10. Missing the role “coating agent” (the role of for example serum albumin
and fibronectin)
11. Change ‘mode of action’ to ‘mechanism of action’ ?
12. Both in-house and within ChEMBL ‘positive allosteric modulation’ and
‘negative allosteric modulation’ is used. Could these be added as
subclasses to ‘allosteric modulation’?
13. ‘Allosteric inhibition’, ‘allosteric activation and ‘allosteric
agonism’ (allosteric agonism and full agonism are misspelled in my version of
BAO) are part of the ontology, could ‘allosteric antagonism’ be added as
well?
14. It would be useful to discuss if the ion channel terms ‘opener’ and
‘blocker’ should be part of the ontology.
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 7:36
We need to clean up and properly define the various cell viability assays, cell growth, viability, proliferation, cell death, etc and how we define mode of action and the endpoint for these.
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/1
Reported by Stephan Schurer
Comment?
'has biosafety level' should be an object property and not a data property;
classes BSL1, 2, 3, 4 should be added back to BAO ideally using the same
original IDs.
What version of the product are you using? On what operating system?
BAO 2.0
Please provide any additional information below.
http://www.bioassayontology.org/bao#BAO_0002826 'has biosafety
level' topDataProperty->'has biosafety level'
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 5:35
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/4
cytokine secretion assay is repeated twice (Reported by Caty Chung on Sep 11,
2013 at 3:06 PM)
BAO_0003003 'cytokine secretion assay'
1) topBAOClass->'assay bioassay component'->bioassay->'signal transduction
assay'->'Cue Signal Response assay'->'cytokine secretion assay'
2) topBAOClass->'assay bioassay component'->bioassay->'signal transduction
assay'->'cytokine secretion assay'
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 5:59
Revisit this issue and make a final call
from this document: https://docs.google.com/spreadsheets/d/1Bc23aYh1T3cN35AHv34no0aVEmbSls_SDYr8cMbNWMw/edit#gid=1016292381
To the example assays listed, please add the following:
Assay_has signal direction_ some_ signal direction
Assay _ has normalization method _ some _ add each assay’s normalization method
The term "Fluorescence Polarization" (currently assay method component --> physical detection method --> fluorescence method, http://www.bioassayontology.org/bao#BAO_0000003) would fit better in the tree under immunoassay-->ex situ immunoassay (http://www.bioassayontology.org/bao#BAO_0000466) and renamed to "Fluorescence Polarization Assay".
While fluorescence polarization is technically a process/method that is exploited in the assay, it seems to be very specific to a subtype of immunoassay, similarly to ELISA, rather than a more generalized reaction or process.
Kits could be categorized by type. We have a bit of this, ie: with the Promega GLO assays. Are there similar types oforganization?
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/5
Reported by Chung, Caty on Mon, Sep 9, 2013 at 12:26 PM
Where in BAO 2.0 do we have the cell lines displayed in
life.ccs.miami.edu<http://life.ccs.miami.edu> (Browse Tree:
http://life.ccs.miami.edu/life/browse)?
In LIFEwrx I see the cell lines, classified by tissue type.
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 6:04
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/7
Reported by Stephan Schurer (with email exchange Anna Gaulton.)
Summary:
-blood qualifies as tissue, or more correctly connecting tissue
-plasma, should be under cell-free (mostly water with protein and some other
non-cellular substances).
-also import the UBERON terms and you can annotate the specific terms when
needed. these would go under biology component > anatomical entity
there are also some assays performed in serum, so worth adding this too
double check if there are any other types of fluids needed; most of the others
are probably ‘organism-based’ assays though (e.g., cerebrospinal fluid) so
wouldn’t need a format term
BAO contains 'blood plasma' from Uberon and we can also add bloodHowever, I
understand this is not what you need as for BAO assay format (model system) we
want a more generic categorySuggest to be consistent with UBERONs
classification.
Uberon classifies tissue:
anatomical entity > material anatomical entity > anatomical structure >
multicellular anatomical structure > tissueand blood (and plasma):
anatomical entity > material anatomical entity > portion of organism substance
> haemolymphatic fluid > blood
anatomical entity > material anatomical entity > portion of organism substance
> haemolymphatic fluid > blood plasma(and there are of course other
definitions, i.e. blood plasma part of some blood)
This classification suggests that assay format for blood and plasma should be
different from cell-based, cell-free, tissue-based.
May have to come up with a new format; more research needed.
Agree that the bio-distribution assay is organism-based; sounds like
pharmacology.
#######
Qiong checked the terms associated with "blood" and "plasma" in our current BAO
2.0:
topBAOClass->'anatomical entity'->'blood plasma'
topBAOClass->'assay bioassay component'->bioassay->'membrane potential
assay'->'plasma membrane potential assay'
topBAOClass->'assay biology component'->'anatomical entity'->'blood plasma'
topBAOClass->'assay biology component'->cellular_component->'plasma membrane'
topBAOClass->cellular_component->'plasma membrane'
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 7:15
bao#, which make it difficult or impossible to resolve the IRI (server does not seem to get the info after the #).
change all URIs and make one or more files of all deprecated terms with the forward link.
OB-git#67 could be categorized by type (ie: microscopes). This would make the tree easier to navigate.
Hierarchies like assay, detection, and design method are not precise and could be updated.
Don't know if this is interesting for you, but the Bioportal displays the term "ATP quantitation using luciferase" in class "assay desig method" as well as in subclass "viability measurement method" - "ATP quantitaion".
I don't know why this happens. In the owl file bao_vocabulary_method.owl the term is define only for subclass "ATP quantitation"
Ontology lookup service displays the correct hierarchy.
Change the term subtree and edit axioms that has that term accordingly.
BioPortal submission table shows:
12/16/2016 version 2.0
BioPortal picks up the version from the .owl from:
http://www.bioassayontology.org/bao/bao_complete.owl
section:
owl:versionInfo2.0</owl:versionInfo>
rdfs:commentCreated by:
Hande Küçük McGinty, Janice Kranz, Joseph Ostrow, Alex Clark, Yu Lin, Saminda Abeyruwan, Uma Vempati, Kunie Sakurai, Vance Lemmon, Ubbo Visser, Stephan Schurer</rdfs:comment>
rdfs:commentsvn: 2986</rdfs:comment>
rdfs:commentRelease date: November 18, 2014</rdfs:comment>
missing terms and axioms discussed previously from the document: https://docs.google.com/spreadsheets/d/1fn-82U_yTs6ZN_mmGzYTiS8TpMxUEzpPKhlOgoNJIJA/edit#gid=2028020569 for LINCS assays ( forwarded email about the discussions)
Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/2
From Stephan (15/May/14 11:01 AM):
'mode of action' is supposed to describe what a compound does with the protein
target, i.e. what's the effect, vs 'mechanism of action' is typically
understood as what the compound does overall in a biological system, i.e. what
is the mechanism that results in a phenotypic change. In that sense, mode of
action would be a component to describe mechanism of action, but mechanism of
action includes more, I don't think one have it as one class.
I agree that the phenotypic mode of action does not fit there well; looks like
somebody added these w/o fully understanding it. We have to look at this.
From Linda:
I find it a bit confusing with the ‘mode of action’ label on the class that
rather, as I understand it, describes the mechanism of action. I am also a
little puzzled by the ‘second messenger assay’ and the’ second messenger
redistribution assay’ class that seems to be equivalent. Also, the subclasses
‘cAMP redistribution assay’ and ‘IP1 redistribution assay’ suggest that
there is a redistribution of these second messengers.
What is the reason for using these labels?
Original issue reported on code.google.com by [email protected]
on 2 Feb 2015 at 5:42
ELISA is classified under "molecular redistribution" and "binding assessment method"
From Vas:
Remove ELISA from the “molecular redistribution” branch. Most of the time ELISA is performed on lysated cells so the there is really no cell structure there to observe.
Ex situ immunoassay is not a term widely used so I don’t know what exactly does that term entail but will look into it.
IHC could be used under the “molecular redistribution” branch. An easy example to explain immunohistochemistry assays would be: You take and freeze the tissue of interest, slice it in thin layers (with a fancy blade / laser) and take one slice and stain it with antibodies. The slice of the tissue you are observing has preserved the cell structure (its not a cell lysate) so you could see an image of the cells locations and also what antibodies are in which cells etc.
In summary in would make sense: ELISA => only under "binding assessment method”, IHC => under both “molecular redistribution” and "binding assessment method”.
The term "Thermal Shift" (currently under assay method component --> physical detection method --> fluorescence method; http://www.bioassayontology.org/bao#BAO_0000058) should be moved to the assay method tree under assay method design --> binding assessment method (http://www.bioassayontology.org/bao#BAO_0000123) and renamed to "Thermal Shift Assay"
While thermal shift assays so often use a fluorescence reporter/detection method, the actual process of thermal shift can be tested with a multitude of proteins, small molecules, etc., with a output that is often measured by fluorescence. Thus, the process itself should be moved to a more appropriate location.
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".
In Bioportal http://www.bioassayontology.org/bao#BAO_0000179 is named result
in OLS it is named endpoint
There is a confusing structure defined for subclass "concentration response endpoint". AC50 is defined as:
"The effective concentration of a perturbagen, which produces 50% of the maximal possible response, which could mean either activation (EC50) or inhibition (IC50) for that perturbagen." Thus it should be parent of EC50 and IC50 which is shown using OLS. But in Bioportal EC50 and IC50 is shown as child of concentration response endpoint which is correct according to the subclass definition in owl file (subclass of BAO_0002162). Screenshots:
The same subgrouping should be done for all other ICx and ECx values for consistency.
Another issue is the grouping of MIC, MIC50, MIC 60 and MIC90 as well as for ED, ED25...ED90. I assume MIC50...MIC90 should be subclass of MIC. The same should be for EDx.
Pertubagen is an important concept in bioassay.
Pertubagen is a role in BAO, which can be beared by multiple entities.
According to this paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086130/): perturbations are chemical reagents including drugs, ligands and other small molecules applied at different time points and doses.
Above indicates that drug, ligand and small molecules can be pertubagen.
Suggestion: To create a has_pertubagen which directly link assay to any entities serves as a pertubagen.
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We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.