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[bioontology-support] Question about Mappings

Manuel Salvadores Olaizola manuelso at stanford.edu
Mon Mar 2 14:42:22 PST 2015


David,

The issue about mapping duplicates is now fixed in BioPortal.

Best,

Manuel

----- Original Message -----
From: "Manuel Salvadores Olaizola" <manuelso at stanford.edu>
To: "durdiales" <durdiales at lcc.uma.es>
Sent: Monday, February 23, 2015 5:50:56 PM
Subject: Re: [bioontology-support] Question about Mappings

This looks like similar to the problem you initially reported. We are fixing it for the next release.

Manuel

----- Original Message -----
From: "durdiales" <durdiales at lcc.uma.es>
To: "Manuel Salvadores Olaizola" <manuelso at stanford.edu>, durdiales at lcc.uma.es
Sent: Thursday, February 19, 2015 3:11:02 PM
Subject: Re: [bioontology-support] Question about Mappings

Hi Manuel,

Many thanks for your answer...

Ok, I have skipped dupplicated, but doing it for some ontologies (ex. 
ATO) --> I found only 144 differents mappings:

http://data.bioontology.org/ontologies/ATO/mappings --> using a simple 
Java Code adding to a Set each different "self link" of the 1st class of 
each collection


example: added --> 
http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000108"

....not 267 mapping as you show on page. Ohhhh, so much different!!!


Then, in order to find a possible solution, I have done the following:

1.- I have added to a Set each different "mappings link" of the 1st 
class of each collection:

example: "mappings": 
"http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000108/mappings",


Then I added to a Set each different "self link" of the 2st class of 
each collection


example: added --> 
http://data.bioontology.org/ontologies/NCBITAXON/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNCBITAXON%2F479885",


2.- That done for each different 1st class of each collection of point 
1.

3. Then I have obtain a more similar values that shown on page, but in 
some cases there are so much differences yet...

Example: AEO on page: 4518 mappings --> 3952 using my possible solution


It could be a problem on my java Code, however, looking at others 
mappings numbers for other ontologies on page,

example:   DDNAT ---> 242 mappings
            TADS  ---> 1563 mappings

and accesing REST:   
http://data.bioontology.org/ontologies/DDANAT/mappings  ---> is empty
                      
http://data.bioontology.org/ontologies/TADS/mappings   ---> is empty


Then, it looks like information shown on page is different that using 
REST queries

Do you know what could be happening please?

Many Thanks,

Kind Regards,

David












El 18.02.2015 02:50, Manuel Salvadores Olaizola escribió:
> Hi,
> 
> Our last version of the automatic mappings (i.e LOOM) do not have IDs,
> as oposite to user mappings (REST) that actually do have an ID. This
> is due to the fact that we do not materialized any more automatic
> mappings, it was too big of a dataset to have it materialized. Two
> mappings are the same if they have the same classes and the same type.
> 
> The fact that mapping shows twice is a bug. Sometimes we keep old
> version of some ontologies internally and that generates duplicity in
> the mapping queries. We will create a ticket to fix that. As a
> workaround I suggest to skip duplicates.
> 
> Thanks for reporting this issue,
> 
> Manuel
> 
> ----- Original Message -----
> From: "durdiales" <durdiales at lcc.uma.es>
> To: support at bioontology.org, durdiales at lcc.uma.es
> Sent: Monday, February 9, 2015 6:09:33 AM
> Subject: [bioontology-support] Question about Mappings
> 
> Hello,
> 
> Dear support team of biontology,
> 
>  From one month ago, we are working on a project where we are 
> integrated
> with you using your REST API (http://data.bioontology.org) in order to
> obtain mappings of the ontologies.
> 
> 
> It is working Ok, however, I have one question about mappings:
> 
> I have seen that for example, ATO ontology, accessing suing web, have
> 267 mappings:
> 
> http://bioportal.bioontology.org/mappings --> selecting ATO
> 
> If we accessing using to ATO using:
> 
> http://data.bioontology.org/ontologies/ATO/mappings?apikey=4ac70241-ad36-42db-8261-a65350a291fa&page=6
> 
> it is correct (6 pag with 50 mappings per page) --> aprox 267 mappings
> 
> 
> however, I have looked at them in more datail, and there are mappings
> that look like the same in the collection, for example:
> 
> 
> http://data.bioontology.org/ontologies/ATO/mappings?apikey=4ac70241-ad36-42db-8261-a65350a291fa&page=6
> 
> ATO_0000024 (mapping to) --> Thesaurus.owl#C45289    ---> that appear
> twice
> 
> 
> Each collection has  "id": null --> then:
> 
> How could I detect that for example these two collections are
> differents, please?
> 
> (see below)
> 
> "collection": [
> 
>      {
>          "id": null,
>          "source": "LOOM",
>          "classes": [
>              {
>                  "@id": "http://purl.obolibrary.org/obo/ATO_0000024",
>                  "@type": "http://www.w3.org/2002/07/owl#Class",
>                  "links": {
>                      "self":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024",
>                      "ontology":
> "http://data.bioontology.org/ontologies/ATO",
>                      "children":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/children",
>                      "parents":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/parents",
>                      "descendants":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/descendants",
>                      "ancestors":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/ancestors",
>                      "tree":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/tree",
>                      "notes":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/notes",
>                      "mappings":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/mappings",
>                      "ui":
> "http://bioportal.bioontology.org/ontologies/ATO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024",
>                      "@context": {
>                          "self": "http://www.w3.org/2002/07/owl#Class",
>                          "ontology":
> "http://data.bioontology.org/metadata/Ontology",
>                          "children":
> "http://www.w3.org/2002/07/owl#Class",
>                          "parents":
> "http://www.w3.org/2002/07/owl#Class",
>                          "descendants":
> "http://www.w3.org/2002/07/owl#Class",
>                          "ancestors":
> "http://www.w3.org/2002/07/owl#Class",
>                          "tree": "http://www.w3.org/2002/07/owl#Class",
>                          "notes":
> "http://data.bioontology.org/metadata/Note",
>                          "mappings":
> "http://data.bioontology.org/metadata/Mapping",
>                          "ui": "http://www.w3.org/2002/07/owl#Class"
>                      }
>                  },
>                  "@context": {
>                      "@vocab": "http://data.bioontology.org/metadata/"
>                  }
>              },
>              {
>                  "@id":
> "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45289",
>                  "@type": "http://www.w3.org/2002/07/owl#Class",
>                  "links": {
>                      "self":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289",
>                      "ontology":
> "http://data.bioontology.org/ontologies/NCIT",
>                      "children":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/children",
>                      "parents":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/parents",
>                      "descendants":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/descendants",
>                      "ancestors":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/ancestors",
>                      "tree":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/tree",
>                      "notes":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/notes",
>                      "mappings":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/mappings",
>                      "ui":
> "http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289",
>                      "@context": {
>                          "self": "http://www.w3.org/2002/07/owl#Class",
>                          "ontology":
> "http://data.bioontology.org/metadata/Ontology",
>                          "children":
> "http://www.w3.org/2002/07/owl#Class",
>                          "parents":
> "http://www.w3.org/2002/07/owl#Class",
>                          "descendants":
> "http://www.w3.org/2002/07/owl#Class",
>                          "ancestors":
> "http://www.w3.org/2002/07/owl#Class",
>                          "tree": "http://www.w3.org/2002/07/owl#Class",
>                          "notes":
> "http://data.bioontology.org/metadata/Note",
>                          "mappings":
> "http://data.bioontology.org/metadata/Mapping",
>                          "ui": "http://www.w3.org/2002/07/owl#Class"
>                      }
>                  },
>                  "@context": {
>                      "@vocab": "http://data.bioontology.org/metadata/"
>                  }
>              }
>          ],
>          "process": null,
>          "@id": "",
>          "@type": "http://data.bioontology.org/metadata/Mapping"
>      },
>      {
>          "id": null,
>          "source": "LOOM",
>          "classes": [
>              {
>                  "@id": "http://purl.obolibrary.org/obo/ATO_0000024",
>                  "@type": "http://www.w3.org/2002/07/owl#Class",
>                  "links": {
>                      "self":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024",
>                      "ontology":
> "http://data.bioontology.org/ontologies/ATO",
>                      "children":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/children",
>                      "parents":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/parents",
>                      "descendants":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/descendants",
>                      "ancestors":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/ancestors",
>                      "tree":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/tree",
>                      "notes":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/notes",
>                      "mappings":
> "http://data.bioontology.org/ontologies/ATO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024/mappings",
>                      "ui":
> "http://bioportal.bioontology.org/ontologies/ATO?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FATO_0000024",
>                      "@context": {
>                          "self": "http://www.w3.org/2002/07/owl#Class",
>                          "ontology":
> "http://data.bioontology.org/metadata/Ontology",
>                          "children":
> "http://www.w3.org/2002/07/owl#Class",
>                          "parents":
> "http://www.w3.org/2002/07/owl#Class",
>                          "descendants":
> "http://www.w3.org/2002/07/owl#Class",
>                          "ancestors":
> "http://www.w3.org/2002/07/owl#Class",
>                          "tree": "http://www.w3.org/2002/07/owl#Class",
>                          "notes":
> "http://data.bioontology.org/metadata/Note",
>                          "mappings":
> "http://data.bioontology.org/metadata/Mapping",
>                          "ui": "http://www.w3.org/2002/07/owl#Class"
>                      }
>                  },
>                  "@context": {
>                      "@vocab": "http://data.bioontology.org/metadata/"
>                  }
>              },
>              {
>                  "@id":
> "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45289",
>                  "@type": "http://www.w3.org/2002/07/owl#Class",
>                  "links": {
>                      "self":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289",
>                      "ontology":
> "http://data.bioontology.org/ontologies/NCIT",
>                      "children":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/children",
>                      "parents":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/parents",
>                      "descendants":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/descendants",
>                      "ancestors":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/ancestors",
>                      "tree":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/tree",
>                      "notes":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/notes",
>                      "mappings":
> "http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289/mappings",
>                      "ui":
> "http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C45289",
>                      "@context": {
>                          "self": "http://www.w3.org/2002/07/owl#Class",
>                          "ontology":
> "http://data.bioontology.org/metadata/Ontology",
>                          "children":
> "http://www.w3.org/2002/07/owl#Class",
>                          "parents":
> "http://www.w3.org/2002/07/owl#Class",
>                          "descendants":
> "http://www.w3.org/2002/07/owl#Class",
>                          "ancestors":
> "http://www.w3.org/2002/07/owl#Class",
>                          "tree": "http://www.w3.org/2002/07/owl#Class",
>                          "notes":
> "http://data.bioontology.org/metadata/Note",
>                          "mappings":
> "http://data.bioontology.org/metadata/Mapping",
>                          "ui": "http://www.w3.org/2002/07/owl#Class"
>                      }
>                  },
>                  "@context": {
>                      "@vocab": "http://data.bioontology.org/metadata/"
>                  }
>              }
>          ],
>          "process": null,
>          "@id": "",
>          "@type": "http://data.bioontology.org/metadata/Mapping"
>      },
> 
> 
> 
> With Regards,
> 
> Thanks you very much in advanced
> 
> David Urdiales
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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