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[bioontology-support] programmatic class mappings

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Oct 23 16:54:06 PDT 2018


Hi Ross,

Apologies that it’s likely not clear from any of our documentation that BioPortal only supports bidirectional mappings, e.g., owl:sameAs, skos:closeMatch, skos:exactMatch, etc.

I wasn’t on the team when the mapping functionality was designed and implemented, so unfortunately I can’t provide any historical perspective on why the system was designed in this manner. I’ll ping one of my predecessors and see if he’s able to offer any more detail.

Kind regards,
Jennifer


On Oct 23, 2018, at 8:32 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Thanks very much Jennifer. I’m able to create mappings through the API for rdfs#sameAs which shows up as expected. However, for rdfs#subClassOf the ordering of things doesn’t appear to be respected.

For example, if I want to map something from our ontology (GAMUTS) which we consider to be a “superclass” of an entity from another ontology. So, for example, I’m trying to make a mapping to state that the DOID entity 1003 (pelvic inflammatory disease) is a subClassOf GAMUTS entity “abdominal_or_pelvic_inflammatory_disease”. If I submit the following JSON object:

{"creator":"rwfilice","relation":"http://www.w3.org/2002/07/rdfs#subClassOf","classes":{"http://purl.obolibrary.org/obo/DOID_1003":"DOID","http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease":"GAMUTS"}}

The API doesn’t appear to respect the order in which the classes are submitted – which in some ways is understandable as the classes object is a hash which by definition does not have an order – but is there any way to specify such an order? The same ordering problem occurs if you do what might be considered a more traditional mapping – i.e. a GAMUTS class that is a subclass of some other ontology class.

In either case if you query the mappings for each entity you get the subclass relationship but they are in reverse order depending on which ontology you query. Below is the result of trying to do that superclass mapping I described above. The first class listed is just whatever ontology you query – you don’t get an order that you can infer the subclass relationship from.

Thanks much,
Ross

GAMUTS query (first the GAMUTS entity, then the DOID entity):

{
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "source": "REST",
        "classes": [
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease",
                ….
            },
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003",
                ….
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
}

And the DOID query (first the DOID entity, then the GAMUTS entity):

    {
        "id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "source": "REST",
        "classes": [
            {
                "@id": "http://purl.obolibrary.org/obo/DOID_1003",
                ….
            },
            {
                "@id": "http://www.gamuts.net/entity#abdominal_or_pelvic_inflammatory_disease",
                ….
            }
        ],
        "process": {
            "id": "http://data.bioontology.org/metadata/mapping_processes/-rwfilice-c180dc40-b904-0136-06f6-005056010074",
            "name": "REST Mapping",
            "creator": "http://data.bioontology.org/users/rwfilice",
            "source": null,
            "relation": "http://www.w3.org/2002/07/rdfs#subClassOf",
            "source_contact_info": null,
            "source_name": null,
            "comment": null,
            "date": "2018-10-23T08:18:01-07:00"
        },
        "@id": "http://data.bioontology.org/rest_backup_mappings/c18b9c30-b904-0136-06f7-005056010074",
        "@type": "http://data.bioontology.org/metadata/Mapping"
    },

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, September 25, 2018 8:16 PM
To: Filice, Ross W
Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] programmatic class mappings

** ATTENTION: This email originated from outside of the MedStar network.
** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.


Hi Ross,

My apologies that you’ve had to endure some back and forth with us. We’re a small team and I wasn’t able to look at this in some detail until today. The example code in our repository is outdated in more ways than I thought. I haven’t had time to modify the code, so instead I’ll add some information here about the JSON structure you need to use, along with some screenshots from testing in Postman.

This is the JSON structure that the mappings endpoint is expecting (which is simpler / has less nesting than the older version):

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":"SNOMEDCT"
  }
}

The “classes” hash contains the data for the classes you want to create a mapping between, with the class ID on the left-hand side and the ontology acronym on the right-hand side.

You can also add the “source", “source_name", and “comment" key value pairs as before, but they aren’t required. What I listed above is the minimum structure you need to create the mapping. Here is a another example with the additional pairs added:

{
  "creator" : "http://data.bioontology.org/user/vendetti<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_vendetti&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=L4_PWzlWuJqVirA2Q4AXx-OJrjhtqPLQY1lx6JmW_PM&e=>",
  "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
  "source" : "vendetti",
  "source_name" : "Jennifer's Test Mapping Data",
  "comment" : "Creates a same as mapping between Melanoma (NCIT) and Malignant melanoma (SNOMEDCT)",
  "classes" : {
    "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3224<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C3224&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=yGobnmBJPN1FRkICvn7Qu51fFEGyi-IWwZIQTSMnRiA&e=>" : "NCIT",
    "http://purl.bioontology.org/ontology/SNOMEDCT/2092003<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=ETN-TPslBeHgPaAzs7-kdKhSE4Tj8F1kgLletuHlPds&e=>":”SNOMEDCT"
  }
}


If you want to test this in Postman, you’ll need header information like the following (please enter your API key where I’ve indicated):


<image001.png>


… and here is the body text:


<image002.png>


Clicking the Send button should result in a “201 Created” status with a result that contains the mapping creation date, etc.:


<image003.png>


… and here is what it looks like in BioPortal (you may have to refresh the SNOMEDCT page):


<image004.png>


You can select the Malignant melanoma class in SNOMEDCT:

https://bioportal.bioontology.org/ontologies/SNOMEDCT/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F2092003<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_SNOMEDCT_-3Fp-3Dclasses-26conceptid-3Dhttp-3A__purl.bioontology.org_ontology_SNOMEDCT_2092003&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=zHivVLJLDcMIQFj9sE8C_14WSL_Z9eUbxxMinrNUYvk&e=>

… and click the Class Mappings tab to view this in the production application. I created one of the mappings with a source_name, and one without. I’ll delete the test mappings in a day or two.

Let me know if you’re still having difficulties.

Kind regards,
Jennifer




On Sep 24, 2018, at 6:53 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:

Thanks Jennifer. If I change to classes instead of terms as such:

{
 "creator" : "http://data.bioontology.org/user/rwfilice<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_rwfilice&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=9Kvl2F4iwxRotzPXcZeeuNimPXKgiegqHo8890U7kDU&e=>",
 "relation" : "http://www.w3.org/2002/07/owl#sameAs<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=vcNCh1Nw4meL4EQ-gJhHWLh_zvX9OknSCUAPTM_FWf0&e=>",
 "source" : "rwfilice",
 "source_name" : "rwfilice Mapping Data",
 "comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",
 "classes" : [ {
   "ontology" : "NCIT",
   "class" : [ "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8711<https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=KguElG_zro0KoJR-Tgb6CUu4Ty7E4Ozt68nY482TGE0&e=>" ]
 }, {
   "ontology" : "SNOMEDCT",
   "class" : [ "http://purl.bioontology.org/ontology/SNOMEDCT/372244006<https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwMGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=iXQuP2CRNkCrgrhP7Oq3MZ0tDFrjJAccP31pmt-pj6c&s=J5RkphjbVpl59HJk-oKWEHhgdo8lEq6ZBMvdlM8kk_w&e=>" ]
 } ]
}

I get an Internal Server Error (500)

Any further help would be much appreciated.
Thanks much,
Ross

-----Original Message-----
From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Monday, September 24, 2018 7:32 PM
To: Filice, Ross W
Cc: John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] programmatic class mappings


** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.

Hello Ross,



Yes - I believe the parameter names were changed at some point from terms/term to classes/class. Try making that change and let us know if you’re still experiencing issues. If so, we’ll try to get the example code updated and running without errors.



Kind regards,

Jennifer






On Sep 24, 2018, at 10:37 AM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:





Thanks for the feedback John. When I try to run the API mappings either on my own (using Postman) or using the github repository code - either against my own VM or against NCBO - I get the following error:





{"errors":["Input does not contain classes"],"status":400}





I'm submitting the JSON object as provided by the github code:





{


"creator" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_user_-5BUSER-5D&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=6STmuyUiOafb_uWLYkSt2mTIyHaKiL3gVDLrMrKIQsc&e=",


"relation" : "https://urldefense.proofpoint.com/v2/url?u=http-3A__www.w3.org_2002_07_owl-23sameAs&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=Us_n00uYdUj1Kuc-JAh3-qKYFzu9ceZAcroFlJwYztU&e=",


"source" : "[USER]",


"source_name" : "[USER] Mapping Data",


"comment" : "This mapping creates a same as mapping between melanoma (NCIT) and melanoma (SNOMEDCT)",


"terms" : [ {


  "ontology" : "NCIT",


  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__ncicb.nci.nih.gov_xml_owl_EVS_Thesaurus.owl-23C8711&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=UqkyOgBlOe3WjUviM-z6tPciJiP6RSk-GlRcpDGjtzo&e=" ]


}, {


  "ontology" : "SNOMEDCT",


  "term" : [ "https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.bioontology.org_ontology_SNOMEDCT_372244006&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zr7zRqjEX-U8zL7JfOqCaXBEn945ciIAdROzmtXpbk8&e=" ]


} ]


}





Does the API require "classes" as input rather than "terms"? The API documentation here is pretty sparse on how to create mappings:





https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=0L-lQQvsK-jDeztW7D_LVE_BNUcn65mPKtze9NSKfMM&s=zdeFJDcG0X2vOsvDzI92O7pl69PTFzx1Sw-mnlsYUms&e=





It includes parameters "source" "id" "process" and "classes" without any other information.





Thanks much,


Ross





-----Original Message-----


From: John Graybeal [mailto:jgraybeal at stanford.edu]


Sent: Thursday, August 30, 2018 7:14 PM


To: Filice, Ross W


Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>


Subject: Re: [bioontology-support] programmatic class mappings








** ATTENTION: This email originated from outside of the MedStar network.** DO NOT CLICK links or attachments unless you recognize the sender and know the content is safe.





Hi Ross,











BIoPortal's treatment of mappings is described in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioontology.org_wiki_BioPortal-5FMappings&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=GnyJG9IhOAhKcd-0XaoPbwRzuZO3f_rp2EEtyKKd1Ao&e=.











Regarding which property to use, that may be tricky in this case; it definitely depends on the meaning you are trying to impute. owl:sameAs should definitely work to tell BioPortal two classes *mean* the same thing, but in principal sameAs means that two classes refer to the same exact concept.  At this point it may be safe to say using sameAs is the right choice for an OWL file. (If the file is really SKOS, than pick the appropriate SKOS mapping according to your meaning above. (I think BioPortal uses exactMatch and closeMatch as the mappings that will generate synonyms in BioPortal, but I can't find that documentation at the moment.)











But if you want BioPortal to know about the mappings, you can't just put that relationship in your ontology, you have to submit it as part of your mappings submission. There are other posts in the list on how to do this, for example https://urldefense.proofpoint.com/v2/url?u=http-3A__ncbo-2Dsupport.2288202.n4.nabble.com_bioontology-2Dsupport-2DOntology-2Dmapping-2Dtd4656476.html-23a4656479&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=8qeu58nRRK4T0ufIGcwLUVV8sz4TDhhkn8Smglr84WE&e=:











You can also manually create mappings using our REST API:











https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_documentation-23Mapping&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=ntH4IrIY2zL6OQ7MGO7ZfPUccoqiJ-zNKHPLrbEhqCg&e=











We have example code for programmatically creating mappings in our GitHub sample code repository:











https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ncbo_ncbo-5Frest-5Fsample-5Fcode_blob_master_java_src_CreateMapping.java&d=DwIGaQ&c=RvBXVp2Kc-itN3g6r3sN0QK_zL4whPpndVxj8-bJ04M&r=9H62R19X1jpVhnInqAe8-Qwl57xeN-i9la7k3Du-8B4aLXqGpEBa63WhIVV7lzgm&m=kyaVFl74YmAKvzlPmc90-iieeSDW2H-RrmcE3lxPa5s&s=hYHcQ4it8WT6UpviWZcmaU2-MAG-5anvap4kCQ4pvgI&e=











I hope all this helps.











John

















On Aug 28, 2018, at 12:02 PM, Filice, Ross W <Ross.W.Filice at gunet.georgetown.edu<mailto:Ross.W.Filice at gunet.georgetown.edu>> wrote:











Hi – in an OWL submission what is the appropriate property to map classes across ontologies? I’ve tried owl sameAs but I don’t know that it’s working. Should we be using skos:exactMatch instead? Or other?











And similarly is there a way to map subclasses across ontologies?











Thanks much,





Ross











Ross W. Filice, M.D.





Associate Professor and Chief, Imaging Informatics





Department of Radiology, MedStar Georgetown University Hospital





Chief, Imaging Informatics





MedStar Medical Group Radiology





Clinical Informatics Scientist





National Center for Human Factors in Healthcare, MedStar Institute for Innovation











3800 Reservoir Road NW, CG 201





Washington DC, 20007





202-444-3450 PHONE





202-444-4899 FAX





ross.w.filice at medstar.net<mailto:ross.w.filice at medstar.net>





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========================





John Graybeal





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Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal





Stanford Center for Biomedical Informatics Research





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