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In CMPO there is inconsistency in term naming e.g. under increased amount of stress fibers phenotype (http://www.ebi.ac.uk/ols/ontologies/cmpo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fcmpo%2FCMPO_0000289) one term ends in 'phenotype' but the other two do not.

There are probably other examples of this throughout the ontology.

Not a high priority but would be nice to have naming consistent now before the ontology gets too large.

asymmetric organelle distribution phenotype

From https://elifesciences.org/articles/24060.

Doesn't specifiy which organelles exactly but they are looking at mitochondria and ER

Could be child of
cellular component phenotype

http://www.ebi.ac.uk/cmpo/CMPO_0000259

New terms in spreadsheet attached. Some still under discussion with author.
Author phenotypes are

high nucleus/cell area
low nucleus/cell area
high Neighbor Fraction
low Neighbor Fraction
high local density
low local density
low nuclear roundness
doughnut nuclei
high total YAP/TAZ
low total YAP/TAZ
high YAP/TAZ ratio
low YAP/TAZ ratio

NewCMPOTermsForidr0030.xlsx

The CMPO fits just right for our study. However, the WS method doesn't seem to return any value when being invoked.

I am currently using netbean to import the WSDL as a library named cmpo.

Here is the code I used to invoke the WS-API. The getVersion() does return the correct version information, but the getRootTerms() doesn't return any result other than an empty object of cmpo.Map.

    cmpo.QueryService service = new cmpo.QueryService();
    cmpo.Query q=service.getOntologyQuery();

    System.out.println(q.getVersion());


    cmpo.Map map=q.getRootTerms("cell elongation");
    System.out.println(map.getItem().size()+"");
    for(cmpo.MapItem mi: map.getItem())
    {
        System.out.println(mi.getKey()+" "+mi.getValue());
    }

The test using WebServiceStudio gives the same outputs. The getVersion() works, but the other methods don't.

Thanks in advance.

Best Regards

Kuan Yan

A new study in the Image Data Resource looking at Cytotoxic T lymphocytes (CTL) in tumors has the following phenotypes that we might want to add new CMPO terms for.

1. increased CTL confinement - this is where the cells move around but don't go very far, so I don't think its quite the same as "decreased cell movement distance", CMPO_0000239
2. enhanced CTL killing - related to "cell killing", http://purl.obolibrary.org/obo/GO_0001906
3. enhanced CTL density
4. transient increase in CTL density

I've already mapped:

1. reduced CTL speed - mapped to "decreased cell movement speed"(CMPO_0000240)
2. enhanced CTL proliferation - mapped to "proliferating cells"
   CMPO_0000241

And I think the final 2 phenotypes are beyond the scope of CMPO

1. reduced tumor growth (could be mapped to
   "decreased tumor growth/size", http://purl.obolibrary.org/obo/MP_0003447
2. vessel normalization

Since all definitions on the same class become logically equivalent, we might get some strange inferences such as entities that ('s depends on' some 'cell in vitro') are equivalent to ('bearer of' some 'cell morphology phenotype'). IMHO, multiple definitions on the same class should be avoided in general.

http://www.ebi.ac.uk/cmpo/CMPO_0000020
http://www.ebi.ac.uk/cmpo/CMPO_0000024
http://www.ebi.ac.uk/cmpo/CMPO_0000027
http://www.ebi.ac.uk/cmpo/CMPO_0000102
http://www.ebi.ac.uk/cmpo/CMPO_0000104
http://www.ebi.ac.uk/cmpo/CMPO_0000150
http://www.ebi.ac.uk/cmpo/CMPO_0000163
http://www.ebi.ac.uk/cmpo/CMPO_0000165
http://www.ebi.ac.uk/cmpo/CMPO_0000166
http://www.ebi.ac.uk/cmpo/CMPO_0000176
http://www.ebi.ac.uk/cmpo/CMPO_0000188
http://www.ebi.ac.uk/cmpo/CMPO_0000194
http://www.ebi.ac.uk/cmpo/CMPO_0000219
http://www.ebi.ac.uk/cmpo/CMPO_0000249
http://www.ebi.ac.uk/cmpo/CMPO_0000283
http://www.ebi.ac.uk/cmpo/CMPO_0000290
http://www.ebi.ac.uk/cmpo/CMPO_0000304
http://www.ebi.ac.uk/cmpo/CMPO_0000306
http://www.ebi.ac.uk/cmpo/CMPO_0000414
http://www.ebi.ac.uk/cmpo/CMPO_0000415
http://www.ebi.ac.uk/cmpo/CMPO_0000427
http://www.ebi.ac.uk/cmpo/CMPO_0000429
http://www.ebi.ac.uk/cmpo/CMPO_0000431

Phenotypes from this paper http://dx.doi.org/10.1101/092403

All about enrichment and de-enrichment of sub populations of cells which we have also seen in other HCS papers but perhaps not adequately described. Phenotypes identified are:

enriched for extremely elongated
enriched for slightly elongated
enriched for extremely triangular
enriched for huge
enriched for slightly large
enriched for small asymmetric cells
enriched for multi-nucleate
enriched for telophase/late telophase
enriched for disjoint bright mito
enriched for apoptotic
de-enriched for slightly elongated
de-enriched for extremely elongated
de-enriched for extremely triangular
de-enriched for huge
de-enriched for slightly large
de-enriched for small asymmetric cells
de-enriched for multi-nucleate
de-enriched for telophase/late telophase
de-enriched for disjoint bright mito
slightly low cell density
low cell density
normal cell density