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SciGraph / golr-loader

Convert SciGraph queries into json that can be loaded by Golr
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Add list of orthologs to each gene-phenotype and gene-disease document #16

Closed kshefchek closed 8 years ago

kshefchek commented 8 years ago

When on a gene page, we want to see any phenotype/disease associated with any of its orthologs. At one point we were waiting on upgrading solr to join the orthology/gene-phenotype queries.

However, I think we can get this information if we store a list of orthologs for a gene for each record.

For example, for SHH, we would add: orthologs: ['ZFIN:ZDB-GENE-980526-41', 'ZFIN:ZDB-GENE-980526-166', 'ZFIN:ZDB-GENE-980526-41', 'NCBIGene:716553','NCBIGene:100016531', 'NCBIGene:100557233', 'NCBIGene:42737','NCBIGene:608860', 'NCBIGene:100512749', 'NCBIGene:29499', 'MGI:98297', 'ZFIN:ZDB-GENE-980526-166']

The pattern is: (gene)-[:RO:HOM0000017|RO:HOM0000020]-(ortholog)

cmungall commented 8 years ago

This works.

This fits well within the original conception of golr closures - in GO we have additional closures beyond is-a closures. E.g. we have isa-partof.

Formally this is just an ortholog closure on the subject, the naming convention would be subject_ortholog_closure

cc @kltm

cmungall commented 8 years ago

The minor drawback I was thinking of is that this makes it hard to show the relationship type (1-1 vs generic orthology) in the display as this gets collapsed.

Not a big drawback, and we can always make a closure for each relationship type.

But as a first pass, just collapse the two

kshefchek commented 8 years ago

We could just make a new tab/table for ortholog-phenotypes/disease relationships, or am I misunderstanding?

cmungall commented 8 years ago

Yes, we would have a new tab. The new tab would query subject_ortholog_closure = $id.

However, the specific type of orthology relationship would be lost. Not a big deal on first pass.

kltm commented 8 years ago

I would suggest _subject_orthologclosure iff it is really something that behaves functionally like a closure in other cases. Otherwise, I'd use the _list pattern--the automatic mechanisms will behave slightly differently.

cmungall commented 8 years ago

it is formally the non-reflexive closure of RO:HOM0000017

kltm commented 8 years ago

While this may be technically true, I was under the impression that these were to be treated like a more-or-less unordered list. The lists and closures take slightly different code paths now, that will diverge more in the future. I just want to make sure that it's in the right functional category.

kshefchek commented 8 years ago

@kltm I think you are right, technically a closure, but for practical purposes it can just be an unordered list (we don't need label mappings for example).

cmungall commented 8 years ago

it's a closure, formally and practically

This is true, even with the extensions that will come next to make it more intuitively closure-like (e.g. gene families from panther, so you can facet on phenotypes from mammals)

The labels should also be useful in the basic case

kshefchek commented 8 years ago

Closure it is.

Based on my understanding, labels are not needed because the ortholog label will be in the subject_label of the solr document. The reference gene label (the page we're on) is not needed, just like in the current homolog tab, it would just be repeated in every row.

Faceting on orthologs via gene families sounds interesting, and would make having this a closure worth while.

jnguyenx commented 8 years ago

The orthologs list is added when the subject is a gene, whatever cypher query is executed.

The pattern is: (gene:gene)-[:RO:HOM0000017|RO:HOM0000020*]-(ortholog:gene)

jnguyenx commented 8 years ago

@kltm do I need to update the schema?

org.apache.http.client.HttpResponseException: ERROR: [doc=null] unknown field 'subject_ortholog_closure' at org.apache.http.impl.client.AbstractResponseHandler.handleResponse(AbstractResponseHandler.java:69) at org.apache.http.client.fluent.Response.handleResponse(Response.java:90) at org.apache.http.client.fluent.Response.returnContent(Response.java:97) at org.monarch.golr.GolrWorker.call(GolrWorker.java:79) at org.monarch.golr.GolrWorker.call(GolrWorker.java:25) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

An example input: { "subject_category":"gene", "qualifier":"inferred", "subject_taxon":[ "NCBITaxon:9606" ], "subject_taxon_label":[ "Homo sapiens" ], "subject_taxon_closure":[ "NCBITaxon:9606", "NCBITaxon:9605", "NCBITaxon:207598", "NCBITaxon:9604", "NCBITaxon:314295", "NCBITaxon:9526", "NCBITaxon:314293", "NCBITaxon:376913", "NCBITaxon:9443", "NCBITaxon:314146", "NCBITaxon:1437010", "NCBITaxon:9347", "NCBITaxon:32525", "NCBITaxon:40674", "NCBITaxon:7742", "NCBITaxon:89593", "NCBITaxon:7711", "NCBITaxon:33511", "NCBITaxon:33213", "NCBITaxon:6072", "NCBITaxon:33208", "NCBITaxon:33154", "NCBITaxon:Union_0000024", "NCBITaxon:2759", "NCBITaxon:Union_0000025", "NCBITaxon:131567", "NCBITaxon:Union_0000030", "NCBITaxon:1", "http://www.w3.org/2002/07/owl#Thing", "ERO:0000985", "OBI:0100026", "BFO:0000040", "BFO:0000004", "BFO:0000002", "BFO:0000001", "NCBITaxon:32524", "NCBITaxon:32523", "NCBITaxon:1338369", "NCBITaxon:8287", "NCBITaxon:117571", "NCBITaxon:117570", "NCBITaxon:7776", "OBO:CARO_0010004", "OBO:CARO_0001010", "http://www.ifomis.org/bfo/1.1/snap#MaterialEntity", "http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant", "http://www.ifomis.org/bfo/1.1/snap#Continuant", "http://www.ifomis.org/bfo/1.1#Entity", "http://www.monarchinitiative.org/_fborganismkey226", "FlyBase:FBsp00000004" ], "subject_taxon_closure_label":[ "Homo sapiens", "Homo", "Homininae", "Hominidae", "Hominoidea", "Catarrhini", "Simiiformes", "Haplorrhini", "Primates", "Euarchontoglires", "Boreoeutheria", "Eutheria", "Theria <Mammalia>", "Mammalia", "Vertebrata <Metazoa>", "Craniata <chordata>", "Chordata", "Deuterostomia", "Bilateria", "Eumetazoa", "Metazoa", "Opisthokonta", "Unikonta", "Eukaryota", "Archaea or Eukaryota", "cellular organisms", "cellular organisms or viruses", "root", "Thing", "non viral organism", "organism", "material_entity", "independent continuant", "continuant", "entity", "Amniota", "Tetrapoda", "Dipnotetrapodomorpha", "Sarcopterygii", "Euteleostomi", "Teleostomi", "Gnathostomata <vertebrate>", "organism", "organism or virus or viroid", "material_entity", "independent_continuant", "continuant", "entity", "Homo sapiens", "FlyBase:FBsp00000004" ], "subject_taxon_closure_map":"{\"NCBITaxon:7776\":\"Gnathostomata <vertebrate>\",\"NCBITaxon:1\":\"root\",\"http://www.w3.org/2002/07/owl#Thing\":\"Thing\",\"NCBITaxon:33511\":\"Deuterostomia\",\"NCBITaxon:376913\":\"Haplorrhini\",\"NCBITaxon:314146\":\"Euarchontoglires\",\"NCBITaxon:33154\":\"Opisthokonta\",\"OBO:CARO_0001010\":\"organism or virus or viroid\",\"NCBITaxon:7742\":\"Vertebrata <Metazoa>\",\"NCBITaxon:9605\":\"Homo\",\"NCBITaxon:9606\":\"Homo sapiens\",\"NCBITaxon:1437010\":\"Boreoeutheria\",\"ERO:0000985\":\"non viral organism\",\"http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant\":\"independent_continuant\",\"NCBITaxon:9526\":\"Catarrhini\",\"NCBITaxon:9604\":\"Hominidae\",\"NCBITaxon:207598\":\"Homininae\",\"NCBITaxon:117570\":\"Teleostomi\",\"NCBITaxon:9443\":\"Primates\",\"NCBITaxon:117571\":\"Euteleostomi\",\"http://www.ifomis.org/bfo/1.1/snap#MaterialEntity\":\"material_entity\",\"NCBITaxon:314293\":\"Simiiformes\",\"NCBITaxon:314295\":\"Hominoidea\",\"http://www.monarchinitiative.org/_fborganismkey226\":\"Homo sapiens\",\"BFO:0000004\":\"independent continuant\",\"OBO:CARO_0010004\":\"organism\",\"BFO:0000001\":\"entity\",\"BFO:0000002\":\"continuant\",\"BFO:0000040\":\"material_entity\",\"NCBITaxon:7711\":\"Chordata\",\"NCBITaxon:1338369\":\"Dipnotetrapodomorpha\",\"NCBITaxon:40674\":\"Mammalia\",\"NCBITaxon:8287\":\"Sarcopterygii\",\"NCBITaxon:33213\":\"Bilateria\",\"http://www.ifomis.org/bfo/1.1#Entity\":\"entity\",\"NCBITaxon:32525\":\"Theria <Mammalia>\",\"NCBITaxon:32524\":\"Amniota\",\"NCBITaxon:32523\":\"Tetrapoda\",\"NCBITaxon:Union_0000024\":\"Unikonta\",\"NCBITaxon:Union_0000025\":\"Archaea or Eukaryota\",\"http://www.ifomis.org/bfo/1.1/snap#Continuant\":\"continuant\",\"OBI:0100026\":\"organism\",\"NCBITaxon:9347\":\"Eutheria\",\"NCBITaxon:89593\":\"Craniata <chordata>\",\"NCBITaxon:6072\":\"Eumetazoa\",\"NCBITaxon:131567\":\"cellular organisms\",\"NCBITaxon:2759\":\"Eukaryota\",\"NCBITaxon:33208\":\"Metazoa\",\"FlyBase:FBsp00000004\":\"FlyBase:FBsp00000004\",\"NCBITaxon:Union_0000030\":\"cellular organisms or viruses\"}", "subject_gene":[ "NCBIGene:3690" ], "subject_gene_label":[ "ITGB3" ], "subject_gene_closure":[ "NCBIGene:3690", "SO:0001217", "SO:0000704", "SO:0001411", "SO:0000001", "SO:0000110", "http://www.w3.org/2002/07/owl#Thing", "GENO:0000701", "BFO:0000031", "BFO:0000002", "BFO:0000001", "GENO:0000014", "Orphanet:122704", "HGNC:6156", "OMIM:173470", "ENSEMBL:ENSG00000259753", "ENSEMBL:ENSG00000259207", "KEGG-hsa:3690" ], "subject_gene_closure_label":[ "ITGB3", "protein_coding_gene", "gene", "biological_region", "region", "sequence_feature", "Thing", "sequence feature or collection", "generically dependent continuant", "continuant", "entity", "gene locus", "ITGB3", "ITGB3", "ITGB3", "ENSEMBL:ENSG00000259753", "ENSEMBL:ENSG00000259207", "ITGB3" ], "subject_gene_closure_map":"{\"GENO:0000014\":\"gene locus\",\"BFO:0000031\":\"generically dependent continuant\",\"ENSEMBL:ENSG00000259753\":\"ENSEMBL:ENSG00000259753\",\"GENO:0000701\":\"sequence feature or collection\",\"http://www.w3.org/2002/07/owl#Thing\":\"Thing\",\"ENSEMBL:ENSG00000259207\":\"ENSEMBL:ENSG00000259207\",\"NCBIGene:3690\":\"ITGB3\",\"SO:0000110\":\"sequence_feature\",\"SO:0000001\":\"region\",\"SO:0001411\":\"biological_region\",\"OMIM:173470\":\"ITGB3\",\"SO:0001217\":\"protein_coding_gene\",\"Orphanet:122704\":\"ITGB3\",\"HGNC:6156\":\"ITGB3\",\"SO:0000704\":\"gene\",\"BFO:0000001\":\"entity\",\"BFO:0000002\":\"continuant\",\"KEGG-hsa:3690\":\"ITGB3\"}", "subject_ortholog_closure":[ "NCBIGene:100025359", "MGI:96614", "NCBIGene:403788", "NCBIGene:707247", "NCBIGene:100070376", "MGI:1338035", "NCBIGene:100562379", "NCBIGene:100051266", "NCBIGene:424191", "ZFIN:ZDB-GENE-030131-6022", "NCBIGene:100566496", "NCBIGene:100557339", "NCBIGene:100560980", "NCBIGene:282644", "NCBIGene:715710", "NCBIGene:463282", "NCBIGene:282642", "MGI:96612", "NCBIGene:3696", "NCBIGene:100505984", "NCBIGene:35368", "NCBIGene:488368", "NCBIGene:100020074", "NCBIGene:257645", "NCBIGene:100053462", "NCBIGene:311061", "NCBIGene:395142", "NCBIGene:100037861", "NCBIGene:100498495", "NCBIGene:362800", "NCBIGene:536286", "NCBIGene:608977", "NCBIGene:475253", "NCBIGene:397063", "NCBIGene:100001836", "NCBIGene:717379", "NCBIGene:700454", "NCBIGene:3693", "NCBIGene:564266", "NCBIGene:459683", "NCBIGene:395470", "NCBIGene:374209", "NCBIGene:556752", "NCBIGene:100022034", "NCBIGene:100009709", "MGI:96615", "NCBIGene:100018731", "NCBIGene:100499533", "NCBIGene:460646", "NCBIGene:100494899" ], "subject":[ "NCBIGene:3690" ], "subject_label":[ "ITGB3" ], "subject_closure":[ "NCBIGene:3690", "SO:0001217", "SO:0000704", "SO:0001411", "SO:0000001", "SO:0000110", "http://www.w3.org/2002/07/owl#Thing", "GENO:0000701", "BFO:0000031", "BFO:0000002", "BFO:0000001", "GENO:0000014", "Orphanet:122704", "HGNC:6156", "OMIM:173470", "ENSEMBL:ENSG00000259753", "ENSEMBL:ENSG00000259207", "KEGG-hsa:3690" ], "subject_closure_label":[ "ITGB3", "protein_coding_gene", "gene", "biological_region", "region", "sequence_feature", "Thing", "sequence feature or collection", "generically dependent continuant", "continuant", "entity", "gene locus", "ITGB3", "ITGB3", "ITGB3", "ENSEMBL:ENSG00000259753", "ENSEMBL:ENSG00000259207", "ITGB3" ], "subject_closure_map":"{\"GENO:0000014\":\"gene locus\",\"BFO:0000031\":\"generically dependent continuant\",\"ENSEMBL:ENSG00000259753\":\"ENSEMBL:ENSG00000259753\",\"GENO:0000701\":\"sequence feature or collection\",\"http://www.w3.org/2002/07/owl#Thing\":\"Thing\",\"ENSEMBL:ENSG00000259207\":\"ENSEMBL:ENSG00000259207\",\"NCBIGene:3690\":\"ITGB3\",\"SO:0000110\":\"sequence_feature\",\"SO:0000001\":\"region\",\"SO:0001411\":\"biological_region\",\"OMIM:173470\":\"ITGB3\",\"SO:0001217\":\"protein_coding_gene\",\"Orphanet:122704\":\"ITGB3\",\"HGNC:6156\":\"ITGB3\",\"SO:0000704\":\"gene\",\"BFO:0000001\":\"entity\",\"BFO:0000002\":\"continuant\",\"KEGG-hsa:3690\":\"ITGB3\"}", "object":[ "DOID:11847" ], "object_label":[ "coronary thrombosis" ], "object_closure":[ "DOID:11847", "MESH:D013927", "MESH:D016769", "MESH:D014652", "DOID:178", "DOID:1287", "DOID:7", "DOID:4", "http://www.w3.org/2002/07/owl#Thing", "OBI:1110055", "BFO:0000016", "BFO:0000017", "BFO:0000020", "BFO:0000002", "BFO:0000001", "UMLS:C0442893", "UMLS:CN200528", "MESH:D004194", "UMLS:C0007222", "MESH:D002318", "UMLS:CN205531", "UMLS:C0042373", "UMLS:CN201558", "UMLS:C0085307", "UMLS:C0087086", "MESH:D003327", "DOID:3393", "DOID:0050828", "UMLS:C0852949", "DOID:114", "UMLS:CN206954", "UMLS:C0018799", "UMLS:CN206932", "MESH:D006331", "UMLS:C0010054", "UMLS:C0010068", "UMLS:C0151744", "MESH:D017202", "UMLS:C0010072", "MESH:D003328" ], "object_closure_label":[ "coronary thrombosis", "Thrombosis", "Embolism and Thrombosis", "Vascular Diseases", "vascular disease", "cardiovascular system disease", "disease of anatomical entity", "disease (DOID)", "Thing", "disease (OBI)", "disposition", "realizable entity", "specifically dependent continuant", "continuant", "entity", "UMLS:C0442893", "UMLS:CN200528", "MESH:D004194", "UMLS:C0007222", "Cardiovascular Diseases", "UMLS:CN205531", "UMLS:C0042373", "UMLS:CN201558", "UMLS:C0085307", "UMLS:C0087086", "Coronary Disease", "coronary artery disease", "artery disease", "UMLS:C0852949", "heart disease", "UMLS:CN206954", "UMLS:C0018799", "UMLS:CN206932", "Heart Diseases", "UMLS:C0010054", "UMLS:C0010068", "UMLS:C0151744", "Myocardial Ischemia", "UMLS:C0010072", "Coronary Thrombosis" ], "object_closure_map":"{\"UMLS:C0852949\":\"UMLS:C0852949\",\"BFO:0000020\":\"specifically dependent continuant\",\"UMLS:C0007222\":\"UMLS:C0007222\",\"DOID:11847\":\"coronary thrombosis\",\"UMLS:C0442893\":\"UMLS:C0442893\",\"DOID:114\":\"heart disease\",\"OBI:1110055\":\"disease (OBI)\",\"UMLS:CN206954\":\"UMLS:CN206954\",\"UMLS:CN206932\":\"UMLS:CN206932\",\"http://www.w3.org/2002/07/owl#Thing\":\"Thing\",\"UMLS:C0151744\":\"UMLS:C0151744\",\"DOID:0050828\":\"artery disease\",\"UMLS:C0010072\":\"UMLS:C0010072\",\"MESH:D014652\":\"Vascular Diseases\",\"DOID:1287\":\"cardiovascular system disease\",\"MESH:D017202\":\"Myocardial Ischemia\",\"UMLS:C0010054\":\"UMLS:C0010054\",\"BFO:0000016\":\"disposition\",\"BFO:0000017\":\"realizable entity\",\"UMLS:C0018799\":\"UMLS:C0018799\",\"MESH:D013927\":\"Thrombosis\",\"UMLS:CN201558\":\"UMLS:CN201558\",\"UMLS:C0085307\":\"UMLS:C0085307\",\"DOID:4\":\"disease (DOID)\",\"DOID:7\":\"disease of anatomical entity\",\"MESH:D006331\":\"Heart Diseases\",\"UMLS:CN200528\":\"UMLS:CN200528\",\"UMLS:CN205531\":\"UMLS:CN205531\",\"DOID:3393\":\"coronary artery disease\",\"MESH:D002318\":\"Cardiovascular Diseases\",\"MESH:D003327\":\"Coronary Disease\",\"MESH:D003328\":\"Coronary Thrombosis\",\"UMLS:C0087086\":\"UMLS:C0087086\",\"UMLS:C0042373\":\"UMLS:C0042373\",\"DOID:178\":\"vascular disease\",\"UMLS:C0010068\":\"UMLS:C0010068\",\"MESH:D004194\":\"MESH:D004194\",\"MESH:D016769\":\"Embolism and Thrombosis\",\"BFO:0000001\":\"entity\",\"BFO:0000002\":\"continuant\"}", "object_category":"disease", "evidence_graph":"{\"nodes\":[{\"id\":\"MONARCH:ed7b4353dd8982aa52d6dfb558430bdb\",\"lbl\":null,\"meta\":{}},{\"id\":\"NCBIGene:3690\",\"lbl\":\"ITGB3\",\"meta\":{}},{\"id\":\"PMID:8598867\",\"lbl\":null,\"meta\":{}},{\"id\":\"_:genid130328\",\"lbl\":\"some variant of ITGB3 that is marker/mechanism for Coronary Thrombosis\",\"meta\":{}},{\"id\":\"ECO:0000033\",\"lbl\":\"traceable author statement\",\"meta\":{}},{\"id\":\"DOID:11847\",\"lbl\":\"coronary thrombosis\",\"meta\":{}}],\"edges\":[{\"sub\":\"MONARCH:ed7b4353dd8982aa52d6dfb558430bdb\",\"obj\":\"DOID:11847\",\"pred\":\"http://purl.org/oban/association_has_object\",\"meta\":{}},{\"sub\":\"MONARCH:ed7b4353dd8982aa52d6dfb558430bdb\",\"obj\":\"PMID:8598867\",\"pred\":\"http://purl.org/dc/elements/1.1/source\",\"meta\":{}},{\"sub\":\"MONARCH:ed7b4353dd8982aa52d6dfb558430bdb\",\"obj\":\"_:genid130328\",\"pred\":\"http://purl.org/oban/association_has_subject\",\"meta\":{}},{\"sub\":\"MONARCH:ed7b4353dd8982aa52d6dfb558430bdb\",\"obj\":\"ECO:0000033\",\"pred\":\"http://purl.obolibrary.org/obo/RO_0002558\",\"meta\":{}},{\"sub\":\"_:genid130328\",\"obj\":\"NCBIGene:3690\",\"pred\":\"http://purl.obolibrary.org/obo/GENO_0000408\",\"meta\":{}},{\"sub\":\"_:genid130328\",\"obj\":\"DOID:11847\",\"pred\":\"http://purl.obolibrary.org/obo/RO_0002607\",\"meta\":{}}],\"meta\":{\"query\":\"monarch:cypher/gene-disease.yaml\"}}", "evidence_object":[ "MONARCH:ed7b4353dd8982aa52d6dfb558430bdb", "NCBIGene:3690", "PMID:8598867", "_:genid130328", "ECO:0000033", "DOID:11847" ], "evidence_object_label":[ "MONARCH:ed7b4353dd8982aa52d6dfb558430bdb", "ITGB3", "PMID:8598867", "some variant of ITGB3 that is marker/mechanism for Coronary Thrombosis", "traceable author statement", "coronary thrombosis" ], "evidence_object_closure":[ "MONARCH:ed7b4353dd8982aa52d6dfb558430bdb", "OBAN:association", "IAO:0000030", "BFO:0000031", "BFO:0000002", "http://www.w3.org/2002/07/owl#Thing", "BFO:0000001", "http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant", "http://www.ifomis.org/bfo/1.1/snap#DependentContinuant", "http://www.ifomis.org/bfo/1.1/snap#Continuant", "http://www.ifomis.org/bfo/1.1#Entity", "NCBIGene:3690", "SO:0001217", "SO:0000704", "SO:0001411", "SO:0000001", "SO:0000110", "http://www.w3.org/2002/07/owl#Thing", "GENO:0000701", "BFO:0000031", "BFO:0000002", "BFO:0000001", "GENO:0000014", "Orphanet:122704", "HGNC:6156", "OMIM:173470", "ENSEMBL:ENSG00000259753", "ENSEMBL:ENSG00000259207", "KEGG-hsa:3690", "PMID:8598867", "IAO:0000013", "IAO:0000310", "SEPIO:0000060", "IAO:0000030", "BFO:0000031", "BFO:0000002", "http://www.w3.org/2002/07/owl#Thing", "BFO:0000001", "http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant", "http://www.ifomis.org/bfo/1.1/snap#DependentContinuant", "http://www.ifomis.org/bfo/1.1/snap#Continuant", "http://www.ifomis.org/bfo/1.1#Entity", "IAO:0000088", "ECO:0000033", "ECO:0000204", "ECO:0000000", "http://www.w3.org/2002/07/owl#Thing", "SEPIO:0000013", "BFO:0000001", "DOID:11847", "MESH:D013927", "MESH:D016769", "MESH:D014652", "DOID:178", "DOID:1287", "DOID:7", "DOID:4", "http://www.w3.org/2002/07/owl#Thing", "OBI:1110055", "BFO:0000016", "BFO:0000017", "BFO:0000020", "BFO:0000002", "BFO:0000001", "UMLS:C0442893", "UMLS:CN200528", "MESH:D004194", "UMLS:C0007222", "MESH:D002318", "UMLS:CN205531", "UMLS:C0042373", "UMLS:CN201558", "UMLS:C0085307", "UMLS:C0087086", "MESH:D003327", "DOID:3393", 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jnguyenx commented 8 years ago

I updated the schema.xml manually... not sure what the best practice is in this case.

kltm commented 8 years ago

For AmiGO/GOlr, we keep the schema (as well as schema generating tools) withing the repo for quick deployment and version tracking.

kltm commented 8 years ago

Yeah, that is a schema-out-of-sync error.

jnguyenx commented 8 years ago

Modifying the schema.xml did fix the error: https://solr-dev.monarchinitiative.org/solr/golr/select?q=subject_ortholog_closure:*

Since we differ with the AmiGO schema, we need to version ours as well. @cmungall have you any plans for that already?

kltm commented 8 years ago

As the hand-rolled (IIRC) metadata that @kshefchek uses to drive the "bbop-js" widgets and the schema for solr are essentially the same, it may be worthwhile to just use owltools to compile down the YAML configurations, a la AmiGO.

cmungall commented 8 years ago

On 4 Jul 2016, at 22:41, Jeremy wrote:

Since we differ with the AmiGO schema, we need to version ours as well. @cmungall have you any plans for that already?

See the makefile for regenerating the schema. We use a different schema but the same framework as GO/Golr

Perhaps this part of the makefile should be converted to gulp?

kshefchek commented 8 years ago

We seem to be capturing paralogs here as well, which maybe isn't a huge deal as a first pass. I suspect it's because we allow a 1 to many relationship on the edge, is there a reason we added this?

cmungall commented 8 years ago

Well that could get confusing if the field is named using the string ortholog.

paralogs could be useful, but could also clutter (unless we re-introduce some of the facets). Also not clear what the impact on the duration of the load-dump cycle is. So perhaps best to start with orthologs.

kshefchek commented 8 years ago

@cmungall it might be too late to reload the gene-phenotype view in time for the various conferences, would it suffice to show these as homolog-phenotype associations in UI and fix this in the next load?

cmungall commented 8 years ago

Yes, I'm assuming this will go in a separate tab?

On 7 Jul 2016, at 14:24, Kent Shefchek wrote:

@cmungall it might be too late to reload the gene-phenotype view in time for the various conferences, would it suffice to show these as homolog-phenotype associations in UI and fix this in the next load?

You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/SciGraph/golr-loader/issues/16#issuecomment-231211739

kshefchek commented 8 years ago

Yes, it's in its own tab.

jnguyenx commented 8 years ago

Okay my bad, now we should not capture the paralogs anymore.

I also updated the yaml configuration for the sorl schema generation in the monarch-app project.