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Communitiy-based Cell Line Ontology

Home Page: https://obofoundry.org/ontology/clo.html

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cell-biology cell-lines obofoundry ontology owl rdf

clo's Introduction

The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on a consensus design pattern.

The website for CLO ontology is here:
https://obofoundry.org/ontology/clo.html  

Reference:

Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer TC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The Cell Line Ontology. Journal of Biomedical Semantics. 2014, 5:37. doi:10.1186/2041-1480-5-37. PMID: 25852852. PMCID: PMC4387853.

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clo's Issues

ro.owl is not found in merged file

In release folder, when opening clo_merged_2013-02-26.owl, the http://www.obofoundry.org/ro/ro.owl is not found.

BAE-BAO Cell Lines

https://drive.google.com/open?id=0B2oTJxSU7CWraEJUcW5BZ2xnT2s
Please see the document for the proposed cell lines from CDD for BAO.

[LINCS] primary cell GM00232

LINCS has GM00232 cell as a primary cell, it is under immortal cell line
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0025503

deprecated term used in CLO

CLO use DOID:disorder (http://purl.obolibrary.org/obo/DOID_0060035) and some of its subClasses that are deprecated in DOID.

Need to fix.

consistent representation of high level cell terms

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/3

By discussion among CL, CLO, OBI developers, we agreed to represent the high 
level cell terms consistently in three ontologies. OBI has been adjusted and 
reuse CL terms. Do we need to review our terms? For example, change permanent 
cell line to immortal cell line cell.

During discussion, it said CLO intends to represent single cell. So, shall we 
use 'cell line cell' rather than 'cell line'?

Original issue reported on code.google.com by [email protected] on 20 Feb 2013 at 5:54

A-375 and A375 are the same cell line, A375 should be a synonym.

http://purl.obolibrary.org/obo/CLO_0001581
http://purl.obolibrary.org/obo/CLO_0001582
-------------------------------------------------------------------------------------------------------------------------------A-375 CLO_0001582
ATCC: CRL-1619
CVCL: CVCL_0132
EFO: EFO_0002103
CHEMBL: CHEMBL3308077

A375 CLO_0001581
HyperCLDB: cl199
http://bioinformatics.hsanmartino.it/hypercldb/cl199.html (corresponds to ATCC: CRL-1619)

LINCS we have
LCL-1235 -> CRL-1619
-> CLO_0001582
-> CHEMBL3308077

"immortal human lung-derived epithelial cell line cell" misclassified

It looks like cells that should be members of the non-existent class "immortal human lung-derived epithelial cell line cell" are now classified under "immortal human septum of telencephalon-derived cell line cell" (obo:CLO_0000488), which is itself incorrectly asserted to be a subclass of "immortal human pancreas-derived cell line cell" (obo:CLO_0000551).

Protege warning log (Illegal redeclarations of entities)

Level: ERROR
Time: 1501036379376
Message: Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000062 in punning not allowed [AnnotationProperty: BFO_0000062, ObjectProperty: BFO_0000062]

Level: ERROR
Time: 1501036379379
Message: Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/BFO_0000063 in punning not allowed [ObjectProperty: BFO_0000063, AnnotationProperty: BFO_0000063]

Level: ERROR
Time: 1501036379379
Message: Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0002222 in punning not allowed [AnnotationProperty: RO_0002222, ObjectProperty: RO_0002222]

Level: ERROR
Time: 1501036379379
Message: Illegal redeclarations of entities: reuse of entity http://purl.obolibrary.org/obo/RO_0000087 in punning not allowed [ObjectProperty: RO_0000087, AnnotationProperty: RO_0000087]

[LINCS] COLO-800

LCL-1233 cell name is COLO-800

a) Two CLO IDs:
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0002561 (exposed in ChEMBL)
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0037121 (newly added by LINCS parsing)

https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?refId=93051123&collection=ecacc_gc

All of the descriptions from HYPERCLDB are a fibroblas from a 14 year old boy:
ECACC catalog code: 93051123
http://bioinformatics.hsanmartino.it/hypercldb/cl852.html
ICLC catalog code: HTL97005
http://bioinformatics.hsanmartino.it/hypercldb/cl854.html
DSMZ catalog code: ACC 193
http://bioinformatics.hsanmartino.it/hypercldb/cl853.html

[CLOSED] wrong species defined in logical axioms

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/4

For examples, 
http://purl.obolibrary.org/obo/CLO_0001056 1205Lu 
which is a mouse cell line defined as human cell line

Original issue reported on code.google.com by [email protected] on 20 Feb 2013 at 8:11

new term request: induced pluripotent stem cell

need to define it as an in vitro cell, definition can consider EFO: induced pluripotent stem cell:
http://www.ebi.ac.uk/efo/EFO_0004905

Origin of the term resource should be recorded in CLO

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/7


I think Cell Line Ontology is great to catalog all the cell lines from 
different resource. However, it would be important to keep the origin of the 
naming in the CLO.

For example, 

[   Class: CCD 1102 KERTr cell
   Term IRI: http://purl.obolibrary.org/obo/CLO_0002240

   Annotations
   alternative term: CCD 1102 KERTr
   seeAlso: ATCC: CRL-2310
   comment: disease: keratinocyte; HPV-16 E6/E7 transformed]

The annotation of this cell line is very poor. Maybe I am lack of background 
information. The origin of this term should be given in the CLO, since CLO 
collects cell lines from different databases. And different databases may have 
different names pointing to same object.

Dose the seeAlso here means this term and CRL-2310 means the same cell line in 
the ontology?

Original issue reported on code.google.com by [email protected] on 3 Oct 2013 at 4:53

[LINCS] T47D

T-47D cell ; T47D cell

http://www.ontobee.org/ontology/LINCS-CLOview?iri=http://purl.obolibrary.org/obo/CLO_0009922
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0009251

http://bioinformatics.hsanmartino.it/hypercldb/cl4454.html

check the definition of 'cell line derived cell line'

This definition needs to be distinct with the definition of cell line.

--- generated at CLO refactory call on 5/26/2015

293 cell should be HEK293 cell

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/12

CLO_0001230 should be updated
293 cell is equal to HEK 293 cell(BTO_0000007;EFO_0001182)

Original issue reported on code.google.com by [email protected] on 29 Apr 2015 at 2:11

BEL-7402 cell line is not in CLO but in BTO

Please double check if it is in CLO with another name.
Otherwise we should add it into CLO.
http://purl.obolibrary.org/obo/BTO_0004050

There are many cell lines existing in BTO but not CLO, we need a programmatic approach to solve this issue.

PANC-1 cell line

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:43 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/1

PANC-1 (http://purl.obolibrary.org/obo/CLO_0008381)
was defined as:
derives from some (cell and (part of some ('septum of telencephalon' and (part 
of some 'Homo sapiens'))))

'septum of telencephalon' is part of brain.

However, PANC-1 is derived from pancreas. Please see:
http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.a
spx?ATCCNum=CRL-1469&Template=cellBiology

The logic definition need to be fixed.

Original issue reported on code.google.com by [email protected] on 16 Jan 2013 at 4:08

[LINCS] SK-MES

The difference is the synonym
SK-MES; SK-MES-1; SK MES 1

Both have the same provider and catalog ID.
seeAlso: ATCC: HTB-58
seeAlso: HyperCLDB: cl4325; ATCC: HTB-58

http://www.ontobee.org/ontology/LINCS-CLOview?iri=http://purl.obolibrary.org/obo/CLO_0009048
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0009049

[CLOSED] Multiple versions of BFO are used

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:43 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/2

CLO imports BFO Graz release. However, there are BFO 1.1 and BFO pre-graz terms 
that may bring in from different imports.

For example, there are process
http://purl.obolibrary.org/obo/BFO_0000007 (BFO pre graz)
http://purl.obolibrary.org/obo/BFO_0000015 (BFO graz release)

http://purl.obolibrary.org/obo/BFO_0000050 part of (BFO graz release)
http://purl.org/obo/owl/OBO_REL#part_of (BFO 1.1)

It should be cleaned up and use single version of BFO

Original issue reported on code.google.com by [email protected] on 20 Feb 2013 at 4:55

new term request: Jump In T-REx HEK 293 cell line

I would like to propose a new entry (probably as child entry to CLO_0037238) for the Jump In T-REx HEK 293 cell line as provided by Thermo: https://www.thermofisher.com/order/catalog/product/A15008#/A15008

Owl file missing almost all information for many ids

In the OWL format file https://raw.githubusercontent.com/CLO-ontology/CLO/master/src/ontology/clo.owl, all ids between CLO_0010001 and CLO_0037010 are lacking all fields, except one subclass. There is much more information on these in the EFO.
Are these data being exported correctly?

cultured cell is under two terms!

The cultured cell in CLO is under two terms:
http://www.ontobee.org/browser/rdf.php?o=CLO&iri=http://purl.obolibrary.org/obo/CL_0000010

This term is from CL, but in CL it has only one mother term: experimentally modified cell in vitro.

Please update the CL_import of CLO.

imported NCBOTaxon terms

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/5

The hierarchy of imported terms look not correct. For example, Mammalia is a 
sibling of Eukaryota. 

Need to check and decide how to import terms from external resources.

Original issue reported on code.google.com by [email protected] on 20 Feb 2013 at 8:22

[LINCS] HUTU-80

Both are from a 53 year old male with adenocarcinoma

http://www.ontobee.org/ontology/LINCS-CLOview?iri=http://purl.obolibrary.org/obo/CLO_0009964
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0004305

http://www.atcc.org/Products/All/HTB-40
http://cancer.sanger.ac.uk/cell_lines/sample/overview?id=907073

RO ID clash

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/10

RO_0002000 'boundary of' and RO_0002002 'has boundary' are being reused for 
other terms in CLO

http://www.ontobee.org/browser/rdf.php?o=CLO&iri=http://purl.obolibrary.org/obo/
RO_0002000 'capable of part of'
http://www.ontobee.org/browser/rdf.php?o=CLOt&iri=http://purl.obolibrary.org/obo
/RO_0002002 'has function in part of'

'capable of part of' ID should be RO_0002216.  'has function in part of' could 
almost certainly be safely mapped to the same relation.

Note - first reported here: 
https://sourceforge.net/p/obo/mailman/message/33261369/

Original issue reported on code.google.com by [email protected] on 23 Jan 2015 at 5:20

Purl redirect for x_import.owl is not functioning correctly

Hi,

I attempted to load CLO.owl in Protege 5.0.0-b17 through the following URLs:
http://purl.obolibrary.org/obo/clo.owl
https://raw.githubusercontent.com/CLO-ontology/CLO/master/src/ontology/clo.owl

However, Protege is unable to resolve the redirects for the various imports you use (e.g. PATO, CL etc...)

Protege attempts to look for (say PATO_import.owl) at http://purl.obolibrary.org/obo/clo/PATO_import.owl, which doesn't exist.

Thanks for looking into this.

Nathaniel

OBO library points to CLO from 2013

https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/clo.yml

products:
- clo.owl: https://raw.githubusercontent.com/CLO-ontology/CLO/master/src/ontology/clo_merged.owl

This is 4 years old! https://github.com/CLO-ontology/CLO/tree/master/src/ontology/release

This has multiple issues due to DOID changing so much, see monarch-initiative/dipper#409

You should make a new merged file.

Additionally you should make a PURL for the unmerged one and make sure purls such as http://purl.obolibrary.org/obo/clo/DOID_import.owl resolve (you will need to create entries in the purl registry above)

Create the dev folder and release folder under scr

We should put the merged file into release folder, and other files into dev folder, otherwise, people will continuously asking the import files questions.

Incorrect logical definition

http://purl.obolibrary.org/obo/CLO_0000266

http://purl.obolibrary.org/obo/CLO_0000266 immortal uterine cervix-derived cell line cell
EquivalentTo: derived from anatomic part some uterine cervix

This is obviously wrong as it includes everything derived from a cervix, not just cell line cells

In general, lack of a genus in a logical definition is a bad smell, including here

Can't find the SK23 cell line in CLO

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/6

I am reading a paper in which a SK23 Cell line was used to construct a melanoma 
vaccine. When I search google, it is easy to tell that SK23 cell is a human 
melanoma cell line.
However, I couldn't find this information in CLO.

The relevant information about this cell line is here:
http://methdb.igh.cnrs.fr/FMPro?-DB=Tissue&-lay=Eingabe&-Format=tissue.html&-op=
bw&tissue===skin%20-%20SK23-MEL%20cells&-Find

So this cell line should be added in CLO.

Original issue reported on code.google.com by [email protected] on 3 Oct 2013 at 4:48

RPMI 6666 cell line contamination according to ICLAC

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/9

See: http://iclac.org/wp-content/uploads/Cross-Contaminations-v7_2.pdf

This information should be integrated with CLO.

The comment for CLO:0008870 is 'disease: Hodgkins disease' (no axioms)

According to iclac, the cell type is EBV+ B-lymphoblastoid

Original issue reported on code.google.com by [email protected] on 19 Oct 2014 at 1:52

OBI: Illumina BeadChip should be deleted from CLO

The OBI term http://purl.obolibrary.org/obo/OBI_0001869 should be deleted from CLO.

Is this project still alive?

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/11

The repo hasn't been updated since 2013, the imports are all stale. It should 
be easy to produce a maintenance release that updates these.

Longer term, what is the strategy for bringing in new content? E..g updates to 
Coriell? Originally this was none by the EBI and then brought into CLO. Is that 
sustainable in the long run?

Original issue reported on code.google.com by [email protected] on 27 Jan 2015 at 7:11

[LINCS] multiple CLO IDs per cell

The following list of cell names have more than one CLO ID.
For examples:
http://www.ontobee.org/search?ontology=LINCS-CLOview&keywords=BALL-1&submit=Search+terms
http://purl.obolibrary.org/obo/CLO_0051004 (CLO):
BALL-1 in Ontobee: LINCS-CLOview
http://purl.obolibrary.org/obo/CLO_0051005 (CLO):
BALL-1 in Ontobee: LINCS-CLOview

[LINCS] SKMEL28

Same cell

http://www.ontobee.org/ontology/LINCS-CLOview?iri=http://purl.obolibrary.org/obo/CLO_0037134
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0009043

seeAlso: ATCC: HTB-72
Reference Source: ATCC HTB-72

textual definitions

Please let me know whether there are any plans to add textual definitions to cell line cell classes that do not already have textual definitions e.g. Caco-2 cell.

add immortalized cell line cell

as a subclass of immortal cell line cell (CLO_0000019)

--- generated at CLO refactory call on 5/26/2015

[LINCS] MCF12A

Same cell, provider and catalog ID.
MCF12A;MCF-12A

http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0007603
http://www.ontobee.org/ontology/LINCS-CLOview?iri=http://purl.obolibrary.org/obo/CLO_0037180

update PURL redirect

Current CLO PURL still redirect to google code, need to change to github one

Replace Deprecated ontology term EFO:0000887

Hi,

The ontology term of "liver" in CLO was mapped to EFO:000087. However, this term has been deprecated and replaced by UBERON_0002107. Could you please update the ontology term accordingly?

Links:
Liver in CLO: https://www.ebi.ac.uk/ols/ontologies/clo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0000887
Liver in EFO: https://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0000887
Liver in UBERON: http://purl.obolibrary.org/obo/UBERON_0002107

Thanks!

Incorrect use of xml schema tag on CLO label

http://purl.obolibrary.org/obo/CLO_0000257

Note that this class has two labels. OntoBee is rendering the Chinese label.

There is an error in the RDF/XML:

   <!-- http://purl.obolibrary.org/obo/CLO_0000257 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CLO_0000257">
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">immortal breast-derived cell line cell</rdfs:label>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#short">永生的乳腺衍生细胞系细胞</rdfs:label>
        <rdfs:label xml:lang="en">immortal breast-derived cell line cell</rdfs:label>
...

xsd:short should only be used with short integers

[LINCS] HeLa modified

modified HeLa cells needs update to the HeLa cell, the genetic transformation, citation.

Cell label Cell CLO ID Parent cell label Parent cell CLO ID Transformation Genetic Modification(s) Reference In use dataset
HeLa ICRP CLO_0009926 HeLa CLO_0003684 Genetic IC-RP (2xIETD) integration IC-RP: Addgene Plasmid #24536 LDS-1222
HeLa ICRP FLIP-L-mCherry CLO_0009929 HeLa CLO_0003684 Genetic IC-RP (2xIETD) and pQCXIP-FLIP-L-mCherry integration IC-RP: Addgene Plasmid #24536; FLIP-L parental plasmid: Inna Lavrik (Otto von Guericke University) LDS-1222
HeLa ICRP FLIP-S-mCherry CLO_0009930 HeLa CLO_0003684 Genetic IC-RP (2xIETD) and pQCXIP-FLIP-S-mCherry integration IC-RP: Addgene Plasmid #24536; FLIP-S parental plasmid: Inna Lavrik (Otto von Guericke University) LDS-1222
HeLa ICRP Bcl-2-mCherry CLO_0009927 HeLa CLO_0003684 Genetic IC-RP (2xIETD) and pQCXIP-Bcl-2-mCherry integration IC-RP: Addgene Plasmid #24536; pQCXIP-Bcl-2-mCherry: John Bachman (Peter Sorger group, Harvard Medical School) LDS-1222
HeLa ICRP Bcl-XL-mCherry CLO_0009928 HeLa CLO_0003684 Genetic IC-RP (2xIETD) and pQCXIP-Bcl-XL-mCherry integration IC-RP: Addgene Plasmid #24536; pQCXIP-Bcl-XL-mCherry: John Bachman (Peter Sorger group, Harvard Medical School) LDS-1222

[LINCS] HME1

Different naming style HME1; hTERT-HME1
Same catalog: ATCC CRL-4010
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0004291
http://www.ontobee.org/ontology/LINCS-CLOview?iri=http://purl.obolibrary.org/obo/CLO_0037172

"comment: disease: TERT immortalized"
This is not a diseased cell line, but normal breast cell line immortalized with hTERT

Missing annotation in HyperCLDB entries

Many cell line cell entries are missing neccessary annotations (organism, cell type, disease, etc). They only contains ATCC xRef via seeAlso property. This is a major fault.

redundant cell line terms

A9 cell:

http://purl.obolibrary.org/obo/CLO_0001618(CLO)
http://purl.obolibrary.org/obo/CLO_0001619(CLO)

A6 cell:

http://purl.obolibrary.org/obo/CLO_0001602(CLO)
http://purl.obolibrary.org/obo/CLO_0001603(CLO)

15C6 cell:

http://purl.obolibrary.org/obo/CLO_0001108(CLO)
http://purl.obolibrary.org/obo/CLO_0001109(CLO)

DS-1 cell:

http://purl.obolibrary.org/obo/CLO_0002821(CLO)
http://purl.obolibrary.org/obo/CLO_0002822(CLO)

GM00425 cell:

http://purl.obolibrary.org/obo/CLO_0003510(CLO)
http://purl.obolibrary.org/obo/CLO_0026109(CLO)

GM00469 cell:

http://purl.obolibrary.org/obo/CLO_0003511(CLO)
http://purl.obolibrary.org/obo/CLO_0025974(CLO)

GM00483 cell:

http://purl.obolibrary.org/obo/CLO_0003512(CLO)
http://purl.obolibrary.org/obo/CLO_0025954(CLO)

GM00638 cell:

http://purl.obolibrary.org/obo/CLO_0003515(CLO)
http://purl.obolibrary.org/obo/CLO_0028878(CLO)

GM00863 cell:

http://purl.obolibrary.org/obo/CLO_0003517(CLO)
http://purl.obolibrary.org/obo/CLO_0029632(CLO)

GM00881 cell:

http://purl.obolibrary.org/obo/CLO_0003518(CLO)
http://purl.obolibrary.org/obo/CLO_0029624(CLO)

GM01229 cell:

http://purl.obolibrary.org/obo/CLO_0003519(CLO)
http://purl.obolibrary.org/obo/CLO_0030283(CLO)

GM01607 cell:

http://purl.obolibrary.org/obo/CLO_0003521(CLO)
http://purl.obolibrary.org/obo/CLO_0031565(CLO)

GM02185 cell:

http://purl.obolibrary.org/obo/CLO_0003522(CLO)
http://purl.obolibrary.org/obo/CLO_0031786(CLO)

GM02290 cell:

http://purl.obolibrary.org/obo/CLO_0003523(CLO)
http://purl.obolibrary.org/obo/CLO_0032129(CLO)

GM02291 cell:

http://purl.obolibrary.org/obo/CLO_0003524(CLO)
http://purl.obolibrary.org/obo/CLO_0032130(CLO)

GM02605 cell:

http://purl.obolibrary.org/obo/CLO_0003526(CLO)
http://purl.obolibrary.org/obo/CLO_0032688(CLO)

GM02824 cell:

http://purl.obolibrary.org/obo/CLO_0003527(CLO)
http://purl.obolibrary.org/obo/CLO_0012748(CLO)

GM02848 cell:

http://purl.obolibrary.org/obo/CLO_0003528(CLO)
http://purl.obolibrary.org/obo/CLO_0012765(CLO)

GM03123 cell:

http://purl.obolibrary.org/obo/CLO_0003529(CLO)
http://purl.obolibrary.org/obo/CLO_0013588(CLO)

GM03252 cell:

http://purl.obolibrary.org/obo/CLO_0003530(CLO)
http://purl.obolibrary.org/obo/CLO_0016698(CLO)

GM05752 cell:

http://purl.obolibrary.org/obo/CLO_0003531(CLO)
http://purl.obolibrary.org/obo/CLO_0024641(CLO)

GM05870 cell:

http://purl.obolibrary.org/obo/CLO_0003532(CLO)
http://purl.obolibrary.org/obo/CLO_0024232(CLO)

GM06127 cell:

http://purl.obolibrary.org/obo/CLO_0003533(CLO)
http://purl.obolibrary.org/obo/CLO_0023661(CLO)

H25B10 cell:

http://purl.obolibrary.org/obo/CLO_0003591(CLO)
http://purl.obolibrary.org/obo/CLO_0003590(CLO)

Hybridoma 234 s.2a cell:

http://purl.obolibrary.org/obo/CLO_0004314(CLO)
http://purl.obolibrary.org/obo/CLO_0004313(CLO)

L368 cell:

http://purl.obolibrary.org/obo/CLO_0007188(CLO)
http://purl.obolibrary.org/obo/CLO_0007187(CLO)

OKT 5 cell:

http://purl.obolibrary.org/obo/CLO_0008254(CLO)
http://purl.obolibrary.org/obo/CLO_0008255(CLO)

P388D subscript(1) cell:

http://purl.obolibrary.org/obo/CLO_0008325(CLO)
http://purl.obolibrary.org/obo/CLO_0008326(CLO)

SC-1 cell:

http://purl.obolibrary.org/obo/CLO_0008957(CLO)
http://purl.obolibrary.org/obo/CLO_0008956(CLO)
http://purl.obolibrary.org/obo/CLO_0008958(CLO)

Sp2/0-Ag14 cell:

http://purl.obolibrary.org/obo/CLO_0009114(CLO)
http://purl.obolibrary.org/obo/CLO_0009115(CLO)

immortal cat cell line cell:

http://purl.obolibrary.org/obo/CLO_0000457(CLO)
http://purl.obolibrary.org/obo/CLO_0000021(CLO)

immortal human cell line cell:

http://purl.obolibrary.org/obo/CLO_0000020(CLO)
http://purl.obolibrary.org/obo/CLO_0000511(CLO)

Error when loading CLO

here is the log:

Error 1 Logged at Mon Jun 22 13:40:11 BST 2015
IOException: Bad ontology library declaration - check logs. Warnings now disabled for this session.
org.protege.editor.owl.model.library.folder.FolderGroupManager.isSuitable(FolderGroupManager.java:123)
org.protege.editor.owl.model.library.OntologyCatalogManager.update(OntologyCatalogManager.java:158)
org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCatalogExists(OntologyCatalogManager.java:116)
org.protege.editor.owl.model.library.OntologyCatalogManager.addFolder(OntologyCatalogManager.java:189)
org.protege.editor.owl.model.OWLModelManagerImpl.addRootFolder(OWLModelManagerImpl.java:353)
org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:309)
org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:190)
org.protege.editor.core.ProtegeManager.loadAndSetupEditorKitFromURI(ProtegeManager.java:207)
org.protege.editor.core.ProtegeApplication.editURI(ProtegeApplication.java:499)
org.protege.editor.core.platform.apple.ProtegeAppleApplication.editFile(ProtegeAppleApplication.java:67)
org.protege.editor.core.platform.apple.AbstractAppleApplicationWrapper$1.invoke(AbstractAppleApplicationWrapper.java:141)
com.sun.proxy.$Proxy0.handleOpenFile(Unknown Source)
com.apple.eawt._AppEventLegacyHandler$5.dispatchEvent(_AppEventLegacyHandler.java:122)
com.apple.eawt._AppEventLegacyHandler.sendEventToEachListenerUntilHandled(_AppEventLegacyHandler.java:168)
com.apple.eawt._AppEventLegacyHandler.openFiles(_AppEventLegacyHandler.java:120)
com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:353)
com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:344)
com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:489)
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
java.awt.EventQueue.access$400(EventQueue.java:82)
java.awt.EventQueue$2.run(EventQueue.java:676)
java.awt.EventQueue$2.run(EventQueue.java:674)
java.security.AccessController.doPrivileged(Native Method)
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)

java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

mistakenly using realizes

Issue by GoogleCodeExporter
Tuesday May 12, 2015 at 11:44 GMT
Originally opened as https://github.com/linikujp/clo-ontology/issues/8

In current CLO, there are two assertions as such:

'adherent cell line culturing' subClassOf: realizes some 'adherent cell culture 
growth mode'
'suspension cell line culturing' subClassOf: realizes some 'suspension cell 
culture growth mode'

The two cell line culturing classes can't be subClassOf realizes some ??? mode.
Since the 'adherent cell culture growth mode' and 'suspension cell culture 
growth mode'are subclasses of quality.
The range of realizes must be 'realizable entity'. Quality is disjoint with 
'realizable entity'. So the above assertion will make the ontology inconsistent.

Solution: Change 'realizes' into 'has_quality'.

Original issue reported on code.google.com by [email protected] on 2 Jun 2014 at 10:07

[LINCS] COLO-679

http://www.ontobee.org/search?ontology=CLO&keywords=+COLO+679&submit=Search+terms

This are the same (female 47 melanoma) :
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0002551
http://www.ontobee.org/ontology/LINCS-CLOview?iri=http://purl.obolibrary.org/obo/CLO_0037120
http://www.ontobee.org/ontology/CLO?iri=http://purl.obolibrary.org/obo/CLO_0050697

Reference:
http://bioinformatics.hsanmartino.it/hypercldb/cl840.html
http://www2.brc.riken.jp/cache/cell/RCB0989

RO_0002161 issue

This term appears both as object property and annotation property.
It is imported from CL.
CL has cleared this bug (obophenotype/cell-ontology#468), but not in CLO.

Sira pointed out the design pattern having the life cycle stage

Sira's message:
cell line part of cell and part_of developmental stage is wrong
i.e. any cell line cell class in CLO that derives_from some cell and (part_of some developmental stage) and part_of some organism
this is wrong
entity is part of entity, process is part of another process but entity cannot be part of a process
I think the correct object property is somewhere in the grouping of this RO term - 'developmentally related to'
or: ‘existence starts during’
derives_from some
(‘cell type’
and (part_of some (‘anatomy’ and (part_of some ( ‘organism’ that bearer_of some disease))
and ‘existence starts during’ some ‘developmental stage’)