bioassayontology / bao

BioAssay Ontology (BAO)

BioAssay Ontology (BAO) is created to establish common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. BAO is a formal OWL-DL ontology and captures deep knowledge about screening assays and their results enabling classifications that enable data analysis and facilitate meaningful retrieval of screening results.

Core concepts/terms

• bioassay
• assay biology
• assay method
• assay format
• assay endpoint
• assay screened entity

Reference

1. Abeyruwan, S.; Vempati, U.; Küçük, H.; Visser, U, Koleti, A.; Mir, A.; Sakurai, K.; Chung, C.; Bittker, J.; Clemons, P.; Brudz, S.; Siripala, A.; Morales, A.; Romacker, M.; Twomey, D.; Bureeva, S.; Lemmon, V., Schürer, S. “Evolving BioAssay Ontology (BAO): Modularization, Integration and Applications” J Biomed Semantics, 2014, doi:10.1186/2041-1480-5-S1-S5.
2. Vempati, U.D.; Przydzial, M.J.; Chung, C.; Abeyruwan, S.; Mir, A.; Sakurai, K.; Visser, U.; Lemmon, V.P.; Schürer, S.C. “Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets using the BioAssay Ontology (BAO).” PLoS One, 2012, doi:10.1371/journal.pone.0049198.
3. Visser U, Abeyruwan S, Vempati U, Smith RP, Lemmon V, Schürer SC. “BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results.” BMC Bioinformatics. 2011 Jun 24;12:257. doi: 10.1186/1471-2105-12-257. PubMed PMID: 21702939; PubMed Central PMCID: PMC3149580.

Terms of use

The data content in git-BioAssay Ontology is licensed under Creative Commons Attribution License Version 4.

Contribute

We are open to collaboration and/or contributions from the community. Any bugs or feature request please submit into git-BioAssay Ontology. This project adheres to the Contributor Covenant code of conduct.

bao's Issues

fluorescence intensity needs to go under endpoint

Change the term subtree and edit axioms that has that term accordingly.

Pharmacological Units

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!

change the lable of KINOMEScan

http://www.bioassayontology.org/bao#BAO_0003109
Add a kit after KINOMEScan.

Discussed on MIAMI ontology meeting (3-4-2016)

signal direction/mode of action clean up

Per discussions a new file is created and new terms created via the discussions need added.

BAO Modeling: A list of questions and suggestions from Linda Zander Balderud

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

assay has signal direction axiom is not there

add the axiom to the definition of term "assay"

Moving Thermal Shift

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.

replacement: bao # into /

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.

missing terms for LINCS

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)

Improve 'mode of action' in BAO OB-git#70

OB-git#70

BAO Modeling: Learning 'blood plasma' annotated in Uberon

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

Typo in BAO ontology description

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".

Missing Import for BAO_NCIT_import.owl

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

ELISA classified under two branches

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”.

missing description for BAO_0002162?

Not sure, but I do not seem able to find it in the repository, and the description for BAO_0002162 seems missing.

BAO Modeling: BAO 2.0 cytokine secretion

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

Invalid character in bao_complete.owl

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.

aleatoric antagonism is still under the wrong subtree

move it to its correct location

Moving of fluorescence polarization

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.

Possible Bioportal issue?

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.

BioPortal 12/16/2016 shows 2.0

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>

Cell Property

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

cell growth, viability, proliferation, etc

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.

Increase the precision of certain hiearchies OB-git#69

OB-git#69

Hierarchies like assay, detection, and design method are not precise and could be updated.

QC Latest BAO release [2.6] #81

OB-git#81

Create new 'mass spectrometry' term OB git-#96

OB git-96

[CLOSED] BAO-PHACTS: BAO end points used in Open PHACTS

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
Activity
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Activity
 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

BAO Modeling: 'mode of action' -vs- 'mechanism of action'

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

BAO Modeling: 'has biosafety level' - would be an object property and not a data property

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

Luminex 100/200 System has mislabeled preferred name as "Luminex 200 Flow Cytometer"

See http://bioportal.bioontology.org/ontologies/BAO/?p=classes&conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0150095

label cleanup for BAO

There are labels with a suffix _bao in the tree, the "_bao" suffix needs removed.

unaddressable URLs

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

Improve 'signal direction' in BAO OB-git#72

OB-git#72

BAO Modeling: Cell line cell in BAO protege and BioPortal

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:

• CatyChungContribution1.png

circular dependency makes it impossible to load the ontology with OWLAPI 5

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"/>

BAO Modeling: Review and re-categorize rename cAMP and cGMP and IP1 redistribution assay

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

Definition of Tethering Assays in BAO OB git #89

OB-git89

Improve 'controls' in BAO OB-git#71

OB-git#71

Axioms related with signal direction

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

Create hierarchy for assay kits OB-git#68

OB-git#68

Kits could be categorized by type. We have a bit of this, ie: with the Promega GLO assays. Are there similar types oforganization?

Pertubagen must link to bioassay

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.

dye and reagent

Dye and reagent are roles.
However, the molecular entity that has a role as a dye or reagent become subclass of dye or reagent as well, which is not ontologically correct.

assinging subclasses for "concentration response 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.

duplicate terms: Biological_process

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>

BAO Modeling: BAO 2.0 Cell Lines

Issue by GoogleCodeExporter
Saturday May 09, 2015 at 11:32 GMT
Originally opened as https://github.com/linikujp/bioassayontology/issues/5

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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

Create hierarchy for detection instruments OB-git#67

OB-git#67 could be categorized by type (ie: microscopes). This would make the tree easier to navigate.

Question about dimensionless units

in subclass dimensionless units terms like "log 10 molar" or "counts per seconds" are listed. Why are they called dimensionless? For consistency all other percentages e.g. "percent dead cells" should also be listed here?

HTS

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

Equilibrium Assay

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/

Difference in OLS and Bioportal

In Bioportal http://www.bioassayontology.org/bao#BAO_0000179 is named result

in OLS it is named endpoint