Package org.openbel.framework.api.internal.KAMStoreDaoImpl

Examples of org.openbel.framework.api.internal.KAMStoreDaoImpl.Namespace

327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
                   edge("geneAbundance(EG:116590)", TRANSCRIBED_TO, "rnaAbundance(EG:116590)"),
                   edge("rnaAbundance(EG:116590)", TRANSLATED_TO, "proteinAbundance(RGD:Mapk1)"),
                   edge("proteinAbundance(RGD:Mapk1)", ACTS_IN, "kinaseActivity(proteinAbundance(RGD:Mapk1))")).create();

        try {
            final Namespace mgi = createNamespace(
                    0,
                    "MGI",
                    "http://resource.belframework.org/belframework/1.0/namespace/mgi-approved-symbols.belns");
            final Namespace eg = createNamespace(
                    1,
                    "EG",
                    "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");
            final Namespace hgnc = createNamespace(
                    2,
                    "HGNC",
                    "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
            final Namespace rgd = createNamespace(
                    3,
                    "RGD",
                    "http://resource.belframework.org/belframework/1.0/namespace/rgd-approved-symbols.belns");

            when(kamstore.getNamespaces(info)).thenReturn(
View Full Code Here
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
                   edge("proteinAbundance(PFR:\"14-3-3 Family\")", ORTHOLOGOUS, "proteinAbundance(PFM:\"14-3-3 Family\")"),
                   edge("proteinAbundance(PFR:\"14-3-3 Family\")", ORTHOLOGOUS, "proteinAbundance(PFH:\"14-3-3 Family\")"),
                   edge("proteinAbundance(PFH:\"14-3-3 Family\")", ORTHOLOGOUS, "proteinAbundance(PFR:\"14-3-3 Family\")")).create();

        try {
            final Namespace pfh = createNamespace(
                    0,
                    "PFH",
                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-protein-families.belns");
            final Namespace pfm = createNamespace(
                    1,
                    "PFM",
                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-protein-families.belns");
            final Namespace pfr = createNamespace(
                    2,
                    "PFR",
                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-protein-families.belns");

            when(kamstore.getNamespaces(info)).thenReturn(
View Full Code Here
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
                   edge("complexAbundance(NCR:\"AP-1 Complex\")", ORTHOLOGOUS, "complexAbundance(NCM:\"AP-1 Complex\")"),
                   edge("complexAbundance(NCR:\"AP-1 Complex\")", ORTHOLOGOUS, "complexAbundance(NCH:\"AP-1 Complex\")"),
                   edge("complexAbundance(NCH:\"AP-1 Complex\")", ORTHOLOGOUS, "complexAbundance(NCR:\"AP-1 Complex\")")).create();

        try {
            final Namespace nch = createNamespace(
                    0,
                    "NCH",
                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-human-complexes.belns");
            final Namespace ncm = createNamespace(
                    1,
                    "NCM",
                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-mouse-complexes.belns");
            final Namespace ncr = createNamespace(
                    2,
                    "NCR",
                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-complexes.belns");

            when(kamstore.getNamespaces(info)).thenReturn(
View Full Code Here
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
            final List<TermParameter> params = kAMStore.getTermParameters(
                    kam.getKamInfo(), term);
            for (final TermParameter p : params) {

                // skip empty namespace, continue
                final Namespace ns = p.getNamespace();
                if (ns == null) {
                    continue;
                }

                // if parameter namespace in rlocs, match
                if (rlocs.contains(ns.getResourceLocation())) {
                    return p;
                }
            }
        }
View Full Code Here
45
46
47
48
49
50
51
        return new BelTerm(id, lbl);
    }

    public static Namespace createNamespace(final Integer id,
            final String prefix, final String resourceLocation) {
        return new Namespace(id, prefix, resourceLocation);
    }
View Full Code Here
TOP

Related Classes of org.openbel.framework.api.internal.KAMStoreDaoImpl.Namespace

  • org.openbel.framework.api.DefaultOrthologize
  • org.openbel.framework.api.internal.KamStoreUtil
  • org.openbel.framework.api.SpeciesKamTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.