clo-ontology / clo Goto Github PK
View Code? Open in Web Editor NEWCommunitiy-based Cell Line Ontology
Home Page: https://obofoundry.org/ontology/clo.html
Communitiy-based Cell Line Ontology
Home Page: https://obofoundry.org/ontology/clo.html
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.
In release folder, when opening clo_merged_2013-02-26.owl, the http://www.obofoundry.org/ro/ro.owl is not found.
https://drive.google.com/open?id=0B2oTJxSU7CWraEJUcW5BZ2xnT2s
Please see the document for the proposed cell lines from CDD for BAO.
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
CLO use DOID:disorder (http://purl.obolibrary.org/obo/DOID_0060035) and some of its subClasses that are deprecated in DOID.
Need to fix.
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
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).
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]
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)
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
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
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
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
This definition needs to be distinct with the definition of cell line.
--- generated at CLO refactory call on 5/26/2015
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
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.
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
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
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
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
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?
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.
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
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
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
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
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)
We should put the merged file into release folder, and other files into dev folder, otherwise, people will continuously asking the import files questions.
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
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
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
The OBI term http://purl.obolibrary.org/obo/OBI_0001869 should be deleted from CLO.
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
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
LIST (shared drive document "LINCS_-all-Xrefs-Ontorat_input-processed.xlsx":
CLO_ID cell name CL_LINCS_ID
http://purl.obolibrary.org/obo/CLO_0051005 BALL-1 LCL-1005
http://purl.obolibrary.org/obo/CLO_0050970 NALM-6 LCL-1007
http://purl.obolibrary.org/obo/CLO_0050143 CCRF-CEM LCL-1012
http://purl.obolibrary.org/obo/CLO_0050992 MOLT-4 LCL-1019
http://purl.obolibrary.org/obo/CLO_0008782 Reh LCL-1039
http://purl.obolibrary.org/obo/CLO_0050406 HCE-T LCL-1047
http://purl.obolibrary.org/obo/CLO_0007094 KG-1 LCL-1056
http://purl.obolibrary.org/obo/CLO_0051561 KG-1a LCL-1057
http://purl.obolibrary.org/obo/CLO_0050999 THP-1 LCL-1072
http://purl.obolibrary.org/obo/CLO_0050123 K-562 LCL-1103
http://purl.obolibrary.org/obo/CLO_0050989 KU812 LCL-1106
http://purl.obolibrary.org/obo/CLO_0051000 KU812E LCL-1107
http://purl.obolibrary.org/obo/CLO_0050974 KU812F LCL-1108
http://purl.obolibrary.org/obo/CLO_0050628 COLO-320 LCL-1174
http://purl.obolibrary.org/obo/CLO_0050632 LoVo LCL-1181
http://purl.obolibrary.org/obo/CLO_0050698 G-361 LCL-1246
http://purl.obolibrary.org/obo/CLO_0050014 BeWo LCL-1293
http://purl.obolibrary.org/obo/CLO_0051535 PC-3 LCL-1299
http://purl.obolibrary.org/obo/CLO_0050924 ME-180 LCL-1305
http://purl.obolibrary.org/obo/CLO_0050637 A172 LCL-1348
http://purl.obolibrary.org/obo/CLO_0050636 T98G LCL-1357
http://purl.obolibrary.org/obo/CLO_0050011 A431 LCL-1404
http://purl.obolibrary.org/obo/CLO_0050810 HOS LCL-1421
http://purl.obolibrary.org/obo/CLO_0050808 MG-63 LCL-1428
http://purl.obolibrary.org/obo/CLO_0050140 Saos-2 LCL-1430
http://purl.obolibrary.org/obo/CLO_0051381 H-EMC-SS LCL-1458
http://purl.obolibrary.org/obo/CLO_0050868 MCF7 LCL-1460
http://purl.obolibrary.org/obo/CLO_0050867 MDA-MB-453 LCL-1485
http://purl.obolibrary.org/obo/CLO_0050910 HeLa LCL-1512
http://purl.obolibrary.org/obo/CLO_0051451 NIH:OVCAR-3 LCL-1522
http://purl.obolibrary.org/obo/CLO_0050930 Ca Ski LCL-1541
http://purl.obolibrary.org/obo/CLO_0050025 A549 LCL-1601
http://purl.obolibrary.org/obo/CLO_0050949 8305C LCL-1685
http://purl.obolibrary.org/obo/CLO_0050951 8505C LCL-1686
http://purl.obolibrary.org/obo/CLO_0050845 5637 LCL-1702
http://purl.obolibrary.org/obo/CLO_0050843 T24 LCL-1709
http://purl.obolibrary.org/obo/CLO_0050102 PANC-1 LCL-1726
http://purl.obolibrary.org/obo/CLO_0050799 HGC-27 LCL-1882
http://purl.obolibrary.org/obo/CLO_0050971 CCRF-HSB-2 LCL-1914
http://purl.obolibrary.org/obo/CLO_0050856 Hep G2 LCL-1925
http://purl.obolibrary.org/obo/CLO_0008957 SC-1 LCL-1944
http://purl.obolibrary.org/obo/CLO_0050268 SK-N-SH LCL-1971
http://purl.obolibrary.org/obo/CLO_0050266 CHP-126 LCL-1973
http://purl.obolibrary.org/obo/CLO_0050081 PEER LCL-2062
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
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.
as a subclass of immortal cell line cell (CLO_0000019)
--- generated at CLO refactory call on 5/26/2015
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
Current CLO PURL still redirect to google code, need to change to github one
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!
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
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
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
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.
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)
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)
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
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
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'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’)
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
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.