RTXteam / RTX

Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)
https://arax.ncats.io/
MIT License
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xDTD perhaps not returning results like we want? #2327

Closed dkoslicki closed 2 weeks ago

dkoslicki commented 1 month ago

any idea why xDTD returns so few results in CI: https://arax.ci.transltr.io/?r=252131 (6 results from xDTD) while in prod it returns many more: https://arax.transltr.io/?r=252133 (41 results from xDTD)

chunyuma commented 1 month ago

@dkoslicki, this is caused by refreshing the xDTD database instead of building a full version.

Although I am not sure what xDTD databases used behind the prod and CI, based on my tests, I think that the xDTD behind prod is ExplainableDTD_v1.0_KG2.8.4.db while the xDTD behind CI may be ExplainableDTD_v1.0_KG2.8.4_refreshedTo_KG2.9.2.db or ExplainableDTD_v1.0_KG2.8.4_refreshedTo_KG2.10.0.db.

As we know, the preferred curie may be different for the same entity in different versions of KG2. For example,

In KG2.8.4

PUBCHEM.COMPOUND:5754 is a preferred curie

PUBCHEM.COMPOUND:5754   Hydrocortisone  biolink:SmallMolecule   HydrocortisoneǂcortisolǂHydrocortisone (JP18/USP/INN)ǂhydrocortisoneǂCortisolǂ17-hydroxycorticosteroneǂHYDROCORTISONEǂ(8S,9S,10R,11S,13S,14S,17S)-11,17-Dihydroxy-17-(2-hydroxyacetyl)-10,13-dimethyl-2,6,7,8,9,11,12,14,15,16-decahydro-1H-cyclopenta[a]phenanthren-3-one  biolink:SmallMoleculeǂbiolink:ChemicalEntityǂbiolink:Drug       Cortisol is the main glucocorticoid secreted by the adrenal cortex and it is involved in the stress response. Its synthetic counterpart hydrocortisone is used, either as an injection or topically, in the treatment of inflammation, allergy, collagen diseases, asthma, adrenocortical deficiency, shock, and some neoplastic conditions. Hydrocortisone is synthesized from pregnenolone and is used as an immunosuppressive drug given by injection in the treatment of severe allergic reactions such as anaphylaxis and angioedema, in place of prednisolone in patients who need steroid treatment but cannot take oral medication, and peri-operatively in patients on long-term steroid treatment to prevent an Addisonian crisis. Cortisol increases blood pressure, blood sugar levels, may cause infertility in women, and suppresses the immune system. The amount of cortisol present in the serum undergoes diurnal variation, with the highest levels present in the early morning and lower levels in the evening, several hours after the onset of sleep. Cortisol is found to be associated with ACTH deficiency and glucocorticoid deficiency, which are inborn errors of metabolism. Cortisol binds to the cytosolic glucocorticoid receptor. After binding the receptor, the newly formed receptor-ligand complex translocates itself into the cell nucleus where it binds to many glucocorticoid response elements (GRE) in the promoter region of the target genes. The DNA-bound receptor then interacts with basic transcription factors, causing the increase in expression of specific target genes. The anti-inflammatory actions of corticosteroids are thought to involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. Specifically, glucocorticoids induce lipocortin-1 (annexin-1) synthesis, which then binds to cell membranes and prevents phospholipase A2 from coming into contact with its substrate arachidonic acid. This leads to diminished eicosanoid production. The cyclooxygenase (both COX-1 and COX-2) expression is also suppressed, potentiating the effect. In other words, the two main products of inflammation, prostaglandins and leukotrienes, are inhibited by the action of glucocorticoids. Glucocorticoids also stimulate the escape of lipocortin-1 into the extracellular space, where it binds to the leukocyte membrane receptors and inhibits various inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, respiratory burst, and the release of various inflammatory mediators (lysosomal enzymes, cytokines, tissue plasminogen activator, chemokines, etc.) from neutrophils, macrophages, and mastocytes. Additionally, the immune system is suppressed by corticosteroids due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin and complement concentrations, the precipitation of lymphocytopenia, and interference with antigen-antibody binding.    DRUGBANK:DB00741ǂPSY:12030ǂDrugCentral:1388ǂCHEBI:180955ǂATC:S02BA01ǂRXNORM:5492ǂHMDB:HMDB0000063ǂNDDF:002147ǂKEGG.COMPOUND:C00735ǂATC:A01AC03ǂATC:D07AA02ǂKEGG.DRUG:D00088ǂPUBCHEM.COMPOUND:5754ǂATC:H02AB09ǂATC:C05AA01ǂUMLS:C0020268ǂNCIT:C2290ǂPSY:23640ǂCAS:50-23-7ǂPathWhiz.Compound:45ǂATC:S01BA02ǂUNII:WI4X0X7BPJǂATC:A07EA02ǂATC:D07XA01ǂCHEBI:17650ǂGTOPDB:2868ǂMESH:D006854ǂINCHIKEY:JYGXADMDTFJGBT-VWUMJDOOSA-NǂATC:S01CB03ǂCHEMBL.COMPOUND:CHEMBL389621    PMID:11413487ǂPMID:2970549ǂPMID:29729985ǂPMID:18666772ǂPMID:2031862ǂPMID:24128814ǂPMID:19256501ǂPMID:27692996ǂPMID:30419492ǂPMID:18289853   biolink:SmallMoleculeǂbiolink:ChemicalEntityOrGeneOrGeneProductǂbiolink:PhysicalEssenceOrOccurrentǂbiolink:MolecularEntityǂbiolink:ChemicalEntityǂbiolink:ChemicalMixtureǂbiolink:Drugǂbiolink:ChemicalOrDrugOrTreatmentǂbiolink:NamedThingǂbiolink:PhysicalEssenceǂbiolink:ChemicalEntityOrProteinOrPolypeptideǂbiolink:MolecularMixtureǂbiolink:OntologyClass

However, in v2.9.2 or v2.10.0, it is not a canonicalized curie anymore.

In KG2.9.2

CHEBI:17650 cortisol    biolink:SmallMolecule   17-hydroxycorticosteroneǂHydrocortisoneǂcortisolǂhydrocortisoneǂCortisolǂHYDROCORTISONE biolink:SmallMoleculeǂbiolink:Drug  http://purl.obolibrary.org/obo/CHEBI_17650  Cortisol is the main glucocorticoid secreted by the adrenal cortex and it is involved in the stress response. Its synthetic counterpart hydrocortisone is used, either as an injection or topically, in the treatment of inflammation, allergy, collagen diseases, asthma, adrenocortical deficiency, shock, and some neoplastic conditions. Hydrocortisone is synthesized from pregnenolone and is used as an immunosuppressive drug given by injection in the treatment of severe allergic reactions such as anaphylaxis and angioedema, in place of prednisolone in patients who need steroid treatment but cannot take oral medication, and peri-operatively in patients on long-term steroid treatment to prevent an Addisonian crisis. Cortisol increases blood pressure, blood sugar levels, may cause infertility in women, and suppresses the immune system. The amount of cortisol present in the serum undergoes diurnal variation, with the highest levels present in the early morning and lower levels in the evening, several hours after the onset of sleep. Cortisol is found to be associated with ACTH deficiency and glucocorticoid deficiency, which are inborn errors of metabolism. Cortisol binds to the cytosolic glucocorticoid receptor. After binding the receptor, the newly formed receptor-ligand complex translocates itself into the cell nucleus where it binds to many glucocorticoid response elements (GRE) in the promoter region of the target genes. The DNA-bound receptor then interacts with basic transcription factors, causing the increase in expression of specific target genes. The anti-inflammatory actions of corticosteroids are thought to involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. Specifically, glucocorticoids induce lipocortin-1 (annexin-1) synthesis, which then binds to cell membranes and prevents phospholipase A2 from coming into contact with its substrate arachidonic acid. This leads to diminished eicosanoid production. The cyclooxygenase (both COX-1 and COX-2) expression is also suppressed, potentiating the effect. In other words, the two main products of inflammation, prostaglandins and leukotrienes, are inhibited by the action of glucocorticoids. Glucocorticoids also stimulate the escape of lipocortin-1 into the extracellular space, where it binds to the leukocyte membrane receptors and inhibits various inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, respiratory burst, and the release of various inflammatory mediators (lysosomal enzymes, cytokines, tissue plasminogen activator, chemokines, etc.) from neutrophils, macrophages, and mastocytes. Additionally, the immune system is suppressed by corticosteroids due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin and complement concentrations, the precipitation of lymphocytopenia, and interference with antigen-antibody binding.    UMLS:C0020268ǂINCHIKEY:JYGXADMDTFJGBT-VWUMJDOOSA-NǂVANDF:4017941ǂCHV:0000006350ǂHMDB:HMDB0000063ǂNDDF:002147ǂPSY:12030ǂDrugCentral:1388ǂPSY:23640ǂCAS:50-23-7ǂATC:S01CB03ǂPUBCHEM.COMPOUND:5754ǂCHEBI:17650ǂATC:C05AA01ǂATC:S01BA02ǂUNII:WI4X0X7BPJǂRXNORM:5492ǂDRUGBANK:DB00741ǂMESH:D006854ǂATC:A07EA02ǂATC:D07AA02ǂATC:A01AC03ǂGTOPDB:2868ǂCHEMBL.COMPOUND:CHEMBL389621ǂPathWhiz.Compound:45ǂATC:S02BA01ǂATC:D07XA01ǂKEGG.DRUG:D00088ǂATC:H02AB09ǂNCIT:C2290 PMID:33600177ǂPMID:8713080ǂPMID:6827553ǂPMID:17374880ǂPMID:36105346ǂPMID:16759088ǂPMID:27396685ǂPMID:27612544ǂPMID:33862517ǂPMID:8474098    biolink:Drugǂbiolink:ChemicalEntityOrProteinOrPolypeptideǂbiolink:OntologyClassǂbiolink:ChemicalOrDrugOrTreatmentǂbiolink:ChemicalMixtureǂbiolink:NamedThingǂbiolink:PhysicalEssenceOrOccurrentǂbiolink:PhysicalEssenceǂbiolink:ChemicalEntityǂbiolink:SmallMoleculeǂbiolink:MolecularEntityǂbiolink:MolecularMixtureǂbiolink:ChemicalEntityOrGeneOrGeneProduct

In KG2.10.0

CHEBI:5783  Hydrocortisone cypionate    biolink:SmallMolecule   hydrocortisone acetate 20 MG/MLǂhydrocortisone Topical Cream [Locoid]ǂhydrocortisone 100 MGǂhydrocortisone cypionateǂhydrocortisone acetate 19 MG/MLǂhydrocortisone butyrate 1 MG/ML Topical Lotionǂhydrocortisone 0.01 MG/MG Rectal Ointmentǂhydrocortisone 25 MG/ML Topical Cream [Proctozone HC]ǂhydrocortisone Topical OintmentǂHemmorexǂhydrocortisone acetate 30 MG [Proctocort]ǂhydrocortisone Rectal Suppository [Proctocort]ǂhydrocortisone acetate 100 MG/ML [Cortifoam]ǂhydrocortisone butyrate 1 MG/ML Topical Solutionǂhydrocortisone valerate 2 MG/ML Topical CreamǂHydrocortisone probutate (USAN)ǂhydrocortisone acetate 0.02 MG/MGǂhydrocortisone 250 MG Injection [Solu-Cortef]ǂhydrocortisone acetate 30 MG Rectal SuppositoryǂHemmorex Rectal Productǂhydrocortisone 0.5 MG [Alkindi]ǂhydrocortisone 0.02 MG/MG Topical Gelǂhydrocortisone 1.67 MG/ML Enemaǂhydrocortisone Enemaǂcortisol cypionateǂhydrocortisone butyrate 1 MG/MLǂhydrocortisone acetate 0.01 MG/MGǂhydrocortisone acetate 25 MG Rectal Suppositoryǂhydrocortisone acetate 0.025 MG/MG Ophthalmic Ointmentǂhydrocortisone butyrate 1 MG/ML Topical CreamǂCortisolǂhydrocortisone valerate 0.002 MG/MG Topical OintmentǂU-Cort Topical Productǂhydrocortisone 1 MG Oral Granules [Alkindi]ǂhydrocortisone 10 MG/ML [Proctocort]ǂhydrocortisone 0.01 MG/MG Topical Gelǂhydrocortisone 0.01 MG/MG [Hemorrodil Plus]ǂhydrocortisone 10 MG/MLǂhydrocortisone Oral Granulesǂhydrocortisone acetate 25 MG [Proctosol]ǂhydrocortisone 10 MG/ML Vaginal Creamǂhydrocortisone sodium phosphate 50 MG/ML Injectable Solutionǂhydrocortisone Topical Gelǂhydrocortisone 10 MGǂhydrocortisone acetate 25 MG Rectal Suppository [Hemmorex]ǂhydrocortisone acetate 25 MG Rectal Suppository [Anusol HC]ǂhydrocortisone Topical Cream [Carmol HC]ǂHydrocortisone valerate (USP)ǂhydrocortisone acetate 10 MG/ML [U-Cort]ǂhydrocortisone acetate 30 MG Rectal Suppository [Proctocort]ǂhydrocortisone 250 MGǂhydrocortisone 20 MG Oral Tablet [Cortef]ǂhydrocortisone Injection [A-Hydrocort]ǂhydrocortisone 0.01 MG/MG Topical Gel [Cortizone]ǂhydrocortisone 2 MG [Alkindi]ǂhydrocortisone 1.67 MG/MLǂhydrocortisone acetate 5 MG/ML Medicated Shampooǂhydrocortisone acetate 0.005 MG/MGǂhydrocortisone butyrate 1 MG/ML Topical Solution [Locoid]ǂhydrocortisone 100 MG [Solu-Cortef]ǂhydrocortisone acetate 23.5 MG/MLǂhydrocortisone valerate 2 MG/MLǂhydrocortisone butyrate 0.001 MG/MG [Locoid]ǂhydrocortisone probutate 1 MG/ML [Pandel]ǂcortisol 17-valerateǂhydrocortisone probutate 1 MG/ML Topical Creamǂhydrocortisone Topical Powderǂhydrocortisone Rectal SuppositoryǂHYDROCORTISONE CYPIONATEǂHYDROCORTISONE HEMISUCCINATEǂhydrocortisone 5 MG/ML Topical Creamǂhydrocortisone 0.02 MG/MGǂhydrocortisone 10 MG/ML Topical Cream [Cortizone]ǂhydrocortisone acetate 25 MG/MLǂhydrocortisone 10 MG/ML Topical Cream [Proctocort]ǂhydrocortisone Topical Cream [Proctocort]ǂHydrocortisone sodium succinate (JP18/USP)ǂhydrocortisone Pillǂhydrocortisone 7.5 MG/MLǂhydrocortisone 100 MG Injectionǂhydrocortisone 10 MG/ML [Scalpicin Itch Relief]ǂhydrocortisone 1 MG/ML Topical Creamǂhydrocortisone butyrate 1 MG/ML Topical Cream [Locoid]ǂhydrocortisone 0.5 MG/MLǂhydrocortisone 1000 MG [Solu-Cortef]ǂhydrocortisone 25 MG/ML Topical Lotionǂhydrocortisone Injectable Suspensionǂhydrocortisone acetate 0.025 MG/MGǂAnusol HC Topical ProductǂHydrocortisone Aceponateǂhydrocortisone 0.01 MG/MG Topical Ointmentǂhydrocortisone 10 mg ORAL TABLETǂhydrocortisone 25 MG/ML Injectable Suspensionǂsolu-cortefǂHydrocortisone Butyrateǂhydrocortisone butyrateǂhydrocortisone Topical Cream [Proctosol]ǂhydrocortisone 10 MG/ML Topical Cream [Hydroskin]ǂhydrocortisone sodium phosphateǂhydrocortisone acetate 20 MG/ML Topical Creamǂhydrocortisone 1000 MGǂCortifoamǂhydrocortisone 20 mg ORAL TABLETǂhydrocortisone 5 MG/ML Topical LotionǂHydrocortisone aceponateǂProctosol Topical ProductǂAlkindi Oral Productǂhydrocortisone Rectal Foamǂhydrocortisone 25 MG/ML [Anusol HC]ǂHydrocortisone acetate (JP18/USP)ǂhydrocortisone acetate 25 MG [Anucort-HC]ǂHydrocortisone aceponate (INN)ǂhydrocortisone 25 MG/ML Topical Cream [Ala-Cort]ǂHydrocortisone butyrate propionateǂScalpicin Itch Reliefǂhydrocortisone butyrate 1 MG/ML [Locoid]ǂCarmol HC Topical Productǂhydrocortisone buteprateǂHemorrodil Plusǂhydrocortisone 0.02 MG/MG Topical Gel [Nuzon]ǂhydrocortisone Ophthalmic Ointmentǂhydrocortisone Topical Lotion [Locoid]ǂhydrocortisone 5 mg ORAL TABLETǂhydrocortisone 100 MG [A-Hydrocort]ǂhydrocortisone Rectal Foam [Cortifoam]ǂhydrocortisone Topical Productǂhydrocortisone Rectal Suppository [Proctosol]ǂhydrocortisone 5 MG [Alkindi]ǂhydrocortisone 5 MGǂhydrocortisone 5 MG/ML Topical Sprayǂhydrocortisone 0.005 MG/MG Topical OintmentǂScalpicin Itch Relief Topical ProductǂSolu-Cortefǂhydrocortisone Injection [Solu-Cortef]ǂhydrocortisone Injectable Productǂhydrocortisone acetate 25 MGǂhydrocortisone butyrate 1 MG/ML Topical Lotion [Locoid]ǂhydrocortisone 25 MG/MLǂhydrocortisone acetate 0.005 MG/MG Ophthalmic Ointmentǂhydrocortisone 0.01 MG/MG Rectal Ointment [Hemorrodil Plus]ǂClinicalm Topical Productǂhydrocortisone acetate 30 MG Rectal Suppository [Hemmorex]ǂHydrocortisone Sodium Phosphateǂhydrocortisone 0.01 MG/MGǂLocoid Topical Productǂaloe polysaccharide / hydrocortisone / iodoquinol Topical Gelǂhydrocortisone 1000 MG Injectionǂhydrocortisone 10 MG/ML Otic Solutionǂhydrocortisone butyrate 0.001 MG/MG Topical Ointment [Locoid]ǂhydrocortisone 25 MG/ML Rectal Creamǂhydrocortisone acetate 25 MG [Hemmorex]ǂhydrocortisone 10 MG/ML Vaginal Cream [Monistat Itch Relief]ǂhydrocortisone acetate 0.01 MG/MG Topical Ointmentǂhydrocortisone Vaginal Creamǂhydrocortisone Medicated Pad or TapeǂHYDROCORTISONEǂhydrocortisone Oral Suspensionǂhydrocortisone acetate 0.01 MG/MG Ophthalmic OintmentǂHYDROCORTISONE PROBUTATEǂhydrocortisone probutate 1 MG/MLǂhydrocortisone 25 MG/ML [Proctosol]ǂHydrocortisone Acetateǂhydrocortisone 5 MG/MLǂAlkindi Granule Productǂhydrocortisone 0.01 MG/MG Topical Ointment [Cortizone]ǂpandelǂhydrocortisone aceponate 1.11 MG/MLǂHydrocortisone butyrateǂhydrocortisone Topical Cream [Pandel]ǂhydrocortisone acetate 10 MG/ML Topical Cream [U-Cort]ǂHYDROCORTISONE VALERATEǂHYDROCORTISONE BUTYRATEǂhydrocortisone acetate 0.00275 MG/MGǂhydrocortisone 10 MG/ML Topical FoamǂHydrocortisoneǂhydrocortisone Ophthalmic Productǂhydrocortisone Vaginal Cream [Vagisil Satin]ǂBiocorneumǂHYDROCORTISONE ACEPONATEǂhydrocortisone 2.5 MG/MLǂcortisol 21-acetateǂanusol hcǂhydrocortisone 10 MG/ML Rectal CreamǂPandel Topical ProductǂLocoidǂAlkindiǂAnucort-HC Rectal Productǂhydrocortisone 10 MG/ML Topical Solution [Scalpicin Itch Relief]ǂhydrocortisone Lozenge ProductǂcortisolǂHemorrodil Plus Rectal Productǂhydrocortisone 25 MG/ML Topical Creamǂa-hydrocortǂhydrocortisone acetate 18.5 MG/MLǂhydrocortisone 1 MG [Alkindi]ǂhydrocortisone 1 MG Oral Granulesǂhydrocortisone Ophthalmic Solutionǂhydrocortisone 1 MG/MG Topical PowderǂVytoneǂhydrocortisone acetate 5 MG/ML Topical Lotionǂhydrocortisone 0.5 MG Oral Granules [Alkindi]ǂhydrocortisone acetate 10 MG/ML [Carmol HC]ǂhydrocortisone 0.025 MG/MG Topical Ointmentǂcortisol 17-butyrateǂhydrocortisone 500 MGǂhydrocortisone acetate 15 MG/MLǂhydrocortisone 0.025 MG/MGǂhydrocortisone 500 MG Injectionǂhydrocortisone 10 MG/ML Topical Solution [Cortizone]ǂhydrocortisone 10 MG/ML Medicated Padǂhydrocortisone Topical Solutionǂhydrocortisone Rectal CreamǂHydrocortisone probutateǂhydrocortisone succinateǂhydrocortisone 25 MG/ML Topical Cream [Procto-Med]ǂhydrocortisone 10 MG/ML Medicated ShampooǂAnusol HCǂhydrocortisone 10 MG/ML Topical Cream [Clinicalm]ǂhydrocortisone Topical Creamǂhydrocortisone 5 MG Oral Granulesǂhydrocortisone 10 MG/ML [Kera-HC]ǂhydrocortisone 0.005 MG/MGǂaloe polysaccharide 0.01 MG/MG / hydrocortisone acetate 0.02 MG/MG / iodoquinol 0.01 MG/MG [Alcortin A]ǂA-Hydrocort Injectable Productǂhydrocortisone 10 MG Oral Tablet [Cortef]ǂhydrocortisone 0.5 MGǂHYDROCORTISONE SODIUM PHOSPHATEǂProctocort Rectal Productǂaloe polysaccharide / hydrocortisone / iodoquinol Topical Gel [Alcortin A]ǂhydrocortisone acetate 5 MG/ML Topical Creamǂhydrocortisone 10 MG Oral Tabletǂhydrocortisone acetate 0.01 MG/MG Topical Gelǂhydrocortisone 0.5 MG Oral Granulesǂhydrocortisone Oral Productǂhydrocortisone Rectal OintmentǂHydrocortisone valerateǂhydrocortisone acetate 10 MG/ML Vaginal Cream [Vagisil Satin]ǂhydrocortisone acetate 30 MG [Hemril]ǂhydrocortisone 1000 MG Injection [Solu-Cortef]ǂHydrocortisone cypionateǂhydrocortisone 25 MG/ML Topical Cream [Proctosol]ǂhydrocortisone 20 MG/ML Topical Lotionǂhydrocortisone Granule Productǂhydrocortisone 10 MG/ML Topical Creamǂhydrocortisone butyrate 0.001 MG/MGǂVytone Topical Productǂhydrocortisone 2 MG/MLǂhydrocortisone 10 MG/ML [Clinicalm]ǂwestcortǂhydrocortisone 10 MG/ML Topical SprayǂHYDROCORTISONE ACETATEǂhydrocortisone Vaginal ProductǂHydrocortisone Sodium SuccinateǂHydrocortisone acetateǂU-Cortǂhydrocortisone 100 MG Injection [Solu-Cortef]ǂhydrocortisone valerate 0.002 MG/MG Topical Ointment [Westcort]ǂhydrocortisone 20 MG/ML Topical Lotion [Nucort]ǂA-Hydrocortǂhydrocortisone Topical Gel [Biocorneum]ǂhydrocortisone 2.5 MGǂKera-HCǂhydrocortisone acetate 10 MG/ML [Vagisil Satin]ǂhydrocortisone 100 MG/ML Injectable Solutionǂhydrocortisone aceponateǂHydrocortisone succinateǂhydrocortisone sodium succinateǂhydrocortisone 10 MG/ML Ophthalmic Solutionǂhydrocortisone acetate 5 MG/ML Topical Sprayǂhydrocortisone probutateǂProctosol Rectal Productǂhydrocortisone Topical Ointment [Westcort]ǂSolu-Cortef Injectable Productǂhydrocortisone enemaǂhydrocortisone Oral Lozengeǂhydrocortisone Topical Ointment [Locoid]ǂhydrocortisone acetate 10 MG/MLǂhydrocortisone hemisuccinateǂhydrocortisone Topical Cream [Kera-HC]ǂhydrocortisone acetate 10 MG/ML Topical CreamǂHydrocortisone Probutateǂhydrocortisone Topical Foamǂhydrocortisone Injectionǂhydrocortisone butyrate 0.001 MG/MG Topical Ointmentǂhydrocortisone Rectal Suppository [Anusol HC]ǂhydrocortisone 0.01 MG/MG Topical Ointment [Aquaphor Itch Relief]ǂCortifoam Rectal Productǂhydrocortisone Oral Tabletǂhydrocortisone acetate 0.01 MG/MG [Biocorneum]ǂhydrocortisone Topical Cream [U-Cort]ǂHydrocortisone 17-butyrateǂhydroxycorticosterone acetateǂhydrocortisone 10 MG/ML Topical Cream [Procto-Pak]ǂhydrocortisone 10 MG/ML Topical Cream [Kera-HC]ǂhydrocortisone 2.5 MG Oral Lozengeǂhydrocortisone-17-butyrateǂHydrocortisone CypionateǂBiocorneum Topical Productǂhydrocortisone 5 MG Oral Tabletǂhydrocortisone acetate 100 MG/MLǂhydrocortisone 15 MG/MLǂhydrocortisone 10 MG/ML Topical Lotion [Cortizone]ǂCarmol HCǂhydrocortisone valerate 0.002 MG/MGǂcortisol sodium phosphateǂhydrocortisone acetate 30 MG [Hemmorex]ǂWestcort Topical ProductǂHydrocortisone Hemisuccinateǂhydrocortisone Oral Granules [Alkindi]ǂhydrocortisone acetate 5 MG/MLǂhydrocortisone 1 MG/MGǂhydrocortisone 10 MG/ML Topical Lotion [Aquanil HC]ǂhydrocortisone acetate 100 MG/ML Rectal Foam [Cortifoam]ǂhydrocortisone acetate 25 MG [Anusol HC]ǂhydrocortisone probutate 1 MG/ML Topical Cream [Pandel]ǂhydrocortisone valerate 0.002 MG/MG [Westcort]ǂhydrocortisone 100 MG/MLǂhydrocortisoneǂhydrocortisone Medicated PadǂClinicalmǂhydrocortisone Otic Solutionǂhydrocortisone 5 MG/ML Medicated ShampooǂAnusol HC Rectal ProductǂAlcortin Aǂhydrocortisone Topical Solution [Scalpicin Itch Relief]ǂhydrocortisone 17-butyrate 21-propionateǂHYDROCORTISONE SODIUM SUCCINATEǂlocoidǂhydrocortisone Topical SprayǂAlcortin A Topical Productǂhydrocortisone acetate 0.0055 MG/MGǂhydrocortisone valerateǂProctocort Topical ProductǂProctosolǂhydrocortisone 1 MGǂhydrocortisone Rectal Ointment [Hemorrodil Plus]ǂhydrocortisone 10 MG/ML Topical Cream [Ala-Cort]ǂhydrocortisone 7.5 MG/ML Topical Lotionǂhydrocortisone 1 MG/MLǂhydrocortisone 20 MG/MLǂhydrocortisone 25 MG/ML Topical Cream [Anusol HC]ǂhydrocortisone 10 MG/ML Topical Solutionǂhydrocortisone 2 MG Oral Granulesǂcortisol succinateǂhydrocortisone Rectal Suppository [Hemmorex]ǂhydrocortisone 500 MG Injection [Solu-Cortef]ǂCortisol 21-acetateǂhydrocortisone acetate 10 MG/ML Vaginal Creamǂhydrocortisone 20 MG/ML Topical Lotion [Ala-Scalp]ǂhydrocortisone 2 MGǂHemril Rectal Productǂhydrocortisone 500 MG [Solu-Cortef]ǂhydrocortisone / iodoquinol Topical Cream [Vytone]ǂhydrocortisone sodium phosphate 50 MG/MLǂhydrocortisone Shampoo ProductǂHydrocortisone Topical Productǂhydrocortisone 25 MG/ML Topical Solution [Texacort]ǂhydrocortisone 2 MG/ML Oral Suspensionǂanucort-hcǂKera-HC Topical Productǂhydrocortisone Rectal Productǂhydrocortisone Rectal Suppository [Anucort-HC]ǂhydrocortisone Topical Cream [Clinicalm]ǂhydrocortisone 20 MG Oral Tabletǂhydrocortisone Otic Productǂhydrocortisone acetate 2 MG/MLǂhydrocortisone acetate 100 MG/ML Rectal Foamǂhydrocortisone Rectal Suppository [Hemril]ǂhydrocortisone acetate 19 MG/ML / iodoquinol 10 MG/ML [Vytone]ǂhydrocortisone 10 MG/ML Topical Lotionǂhydrocortisone 20 MGǂHYDROCORTISONE BUTEPRATEǂVagisil Satin Vaginal ProductǂVagisil Satinǂhydrocortisone acetateǂhydrocortisone 250 MG Injectionǂ17-hydroxycorticosteroneǂhydrocortisone 5 MG Oral Granules [Alkindi]ǂhydrocortisone Medicated Shampooǂhydrocortisone Topical Cream [Anusol HC]ǂhydrocortisone acetate 25 MG Rectal Suppository [Anucort-HC]ǂhydrocortisone 1.67 MG/ML Enema [Cortenema]ǂhydrocortisone 5 MG Oral Tablet [Cortef]ǂProctocortǂhydrocortisone Injectable Solutionǂhydrocortisone Oral Liquid ProductǂHemrilǂAnucort-HCǂWestcortǂhydrocortisone acetate 30 MGǂhydrocortisone 25 MG/ML Topical Solutionǂhydrocortisone 2 MG Oral Granules [Alkindi]ǂHydrocortisone Valerateǂhydrocortisone Topical LotionǂHydrocortisone (JP18/USP/INN)ǂhydrocortisone Topical Solution [Locoid]ǂhydrocortisone 250 MG [Solu-Cortef]ǂPandelǂhydrocortisone acetate 0.01 MG/MG Topical Gel [Biocorneum] biolink:SmallMoleculeǂbiolink:Drug  http://purl.obolibrary.org/obo/CHEBI_5783   "The sodium salt of hydrocortisone succinate with glucocorticoid property. Hydrocortisone sodium succinate is chemically similar to the endogenous hormone that stimulates anti-inflammatory and immunosuppressive activities, in addition to exhibiting minor mineralocorticoid effects. This agent binds to intracellular glucocorticoid receptors and is translocated into the nucleus, where it initiates the transcription of glucocorticoid-responsive genes, such as various cytokines and lipocortins. Lipocortins inhibit phospholipase A2, thereby blocking the release of arachidonic acid from membrane phospholipids and preventing the synthesis of prostaglandins and leukotrienes, both potent mediators of inflammation.; The sodium salt of hydrocortisone succinate with glucocorticoid property. Hydrocortisone sodium succinate is chemically similar to the endogenous hormone that stimulates anti-inflammatory and immunosuppressive activities, in addition to exhibiting minor mineralocorticoid effects. This agent binds to intracellular glucocorticoid receptors and is translocated into the nucleus, where it initiates the transcription of glucocorticoid-responsive genes, such as various cytokines and lipocortins. Lipocortins inhibit phospholipase A2, thereby blocking the release of arachidonic acid from membrane phospholipids and preventing the synthesis of prostaglandins and leukotrienes, both potent mediators of inflammation. Check for ""https://www.cancer.gov/about-cancer/treatment/clinical-trials/intervention/C1819"" active clinical trials using this agent. (""http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C1819"" NCI Thesaurus); UMLS Semantic Type: STY:T109; UMLS Semantic Type: STY:T121"    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UMLS:C0126110ǂUMLS:C0986553ǂRXCUI:1039350ǂRXCUI:406307ǂRXCUI:2657304ǂUMLS:C4056126ǂUMLS:C5840545ǂUMLS:C5835749ǂRXNORM:1489372ǂUMLS:C1125996ǂUMLS:C3833072ǂRXNORM:370646ǂUMLS:C3233896ǂRXCUI:2656919ǂUMLS:C1606857ǂRXCUI:1013097ǂUMLS:C1246466ǂRXCUI:1164010ǂCHV:0000044940ǂRXNORM:1250490ǂPUBCHEM.COMPOUND:16623ǂRXCUI:1542920ǂRXCUI:1314930ǂCHV:0000006350ǂRXNORM:208816ǂUMLS:C3254922ǂRXNORM:2399652ǂNDDF:006704ǂUMLS:C1241571ǂUMLS:C0689112ǂUMLS:C1244666ǂUMLS:C5417539ǂRXCUI:1114852ǂATC:A01AC03ǂPUBCHEM.COMPOUND:5754ǂRXNORM:340099ǂRXNORM:203594ǂUMLS:C3833080ǂRXNORM:1491720ǂRXNORM:1729511ǂRXCUI:1291379ǂRXCUI:446496ǂRXCUI:330460ǂRXNORM:372423ǂVANDF:4025074ǂRXCUI:310869ǂRXCUI:1039281ǂRXCUI:2646817ǂRXNORM:446496ǂUMLS:C1600900ǂRXNORM:1674194ǂRXCUI:2654828ǂCHV:0000044939ǂRXCUI:2649516ǂRXCUI:1291102ǂRXNORM:2399653ǂRXNORM:2533903ǂRXCUI:52147ǂRXNORM:339972ǂUMLS:C2241626ǂRXNORM:1187962ǂRXNORM:1291381ǂUMLS:C0775264ǂUMLS:C5842244ǂRXCUI:2462510ǂUMLS:C0707414ǂRXCUI:1191377ǂUMLS:C2946413ǂRXCUI:1291103ǂNCIT:C61786ǂRXNORM:2399656ǂRXNORM:334971ǂRXNORM:1314928ǂRXNORM:1114852ǂRXNORM:1494035ǂRXCUI:103468ǂUMLS:C3535985ǂUMLS:C3495379ǂRXCUI:2658049ǂRXCUI:2660431ǂRXCUI:1291377ǂVANDF:4017946ǂKEGG.DRUG:D06876ǂRXCUI:543689ǂRXCUI:1738586ǂRXCUI:1314929ǂUMLS:C1236217ǂUMLS:C5841906ǂRXNORM:2533907ǂRXNORM:329837ǂRXCUI:41277ǂRXCUI:1494035ǂRXCUI:1370767ǂRXCUI:1191378ǂRXNORM:1542920ǂCHEMBL.COMPOUND:CHEMBL1200953ǂRXCUI:1187128ǂRXNORM:197787ǂRXCUI:2655245ǂRXCUI:2649527ǂUMLS:C3818673ǂUMLS:C4301580ǂRXNORM:1542921ǂRXNORM:339990ǂRXCUI:377713ǂRXNORM:370648ǂRXCUI:362448ǂRXCUI:250804ǂINCHIKEY:FOGXJPFPZOHSQS-AYVLZSQQSA-NǂUMLS:C4722853ǂUMLS:C3464038ǂUMLS:C0992415ǂDRUGBANK:DB14539ǂUMLS:C4048528ǂUMLS:C0691533ǂUMLS:C1262759ǂRXNORM:310861ǂRXNORM:1865144ǂCHEMBL.COMPOUND:CHEMBL1683ǂRXNORM:2533904ǂUMLS:C4489741ǂKEGG.DRUG:D00978ǂUMLS:C2940735ǂRXCUI:1360948ǂCHEMBL.COMPOUND:CHEMBL1200562ǂRXNORM:1314931ǂRXCUI:235483ǂRXNORM:250804ǂRXNORM:2399644ǂRXNORM:367599ǂUMLS:C5417484ǂUMLS:C5838334ǂRXNORM:1545173ǂKEGG.DRUG:D00088ǂUMLS:C3536165ǂCAS:2203-97-6ǂRXCUI:377723ǂRXNORM:1164013ǂRXNORM:203592ǂRXNORM:1164014ǂINCHIKEY:HHZQLQREDATOBM-CODXZCKSSA-NǂUMLS:C5846090ǂRXCUI:2657258ǂRXCUI:2399653ǂPDQ:CDR0000039861ǂRXCUI:339990ǂRXCUI:376828ǂRXNORM:1370764ǂRXCUI:1235747ǂRXNORM:1370745ǂUMLS:C0701713ǂKEGG.COMPOUND:C02821ǂRXCUI:1184839ǂRXNORM:103401ǂVANDF:4017947ǂUMLS:C4048373ǂRXCUI:316056ǂRXNORM:367412ǂCAS:50-23-7ǂUMLS:C0977607ǂPUBCHEM.COMPOUND:219121ǂUMLS:C4081380ǂRXCUI:2648465ǂRXCUI:329836ǂUMLS:C0977581ǂATC:D07AA02ǂUMLS:C0707421ǂRXCUI:1291081ǂUMLS:C1588800ǂRXNORM:1792288ǂRXCUI:1792289ǂRXNORM:1291081ǂRXCUI:1187962ǂUMLS:C1246471ǂUMLS:C3254919ǂRXCUI:1370746ǂUMLS:C5448265ǂNDDF:005250ǂRXNORM:543689ǂUMLS:C5417520ǂRXCUI:1164004ǂRXCUI:2533906ǂRXNORM:1436948ǂUMLS:C5417563ǂRXNORM:832711ǂRXNORM:1738590ǂRXNORM:543492ǂRXCUI:310861ǂUMLS:C0707409ǂRXCUI:797806ǂDRUGBANK:DB14540ǂRXNORM:1674199ǂRXNORM:197786ǂRXCUI:1291382ǂRXNORM:238754ǂUMLS:C0056387ǂUMLS:C5839095ǂRXCUI:330825ǂRXNORM:1094442ǂRXCUI:1549473ǂRXNORM:1235742ǂRXNORM:2399655ǂUMLS:C1241561ǂUMLS:C4081376ǂUMLS:C4081384ǂVANDF:4017945ǂRXCUI:2647148ǂRXCUI:1164014ǂUMLS:C1251956ǂRXNORM:377305ǂUMLS:C5839110ǂRXNORM:1291091ǂRXNORM:27196ǂRXNORM:1294904ǂRXCUI:1738596ǂNDDF:006405ǂUMLS:C1509921ǂUMLS:C0724382ǂRXCUI:2645362ǂRXNORM:2399660ǂCHV:0000045338ǂDrugCentral:1388ǂRXCUI:1291101ǂRXNORM:1164004ǂRXNORM:1170970ǂRXCUI:1790684ǂRXCUI:1012234ǂRXCUI:1012232ǂRXNORM:1039279ǂRXNORM:1738596ǂCAS:74050-20-7ǂRXCUI:334971ǂRXCUI:1291082ǂRXCUI:197786ǂUNII:O6550D6K3AǂCHEBI:31677ǂUMLS:C0710432ǂRXCUI:310878ǂKEGG.DRUG:D01886ǂUMLS:C4056585ǂRXCUI:2662279ǂRXNORM:1370758ǂPSY:12030  PMID:22664131ǂPMID:24592867ǂPMID:30529634ǂPMID:25443644ǂPMID:35303485ǂPMID:14661924ǂPMID:7473540ǂPMID:27295506ǂPMID:16023372ǂPMID:24128814  biolink:ChemicalOrDrugOrTreatmentǂbiolink:ChemicalEntityOrProteinOrPolypeptideǂbiolink:OntologyClassǂbiolink:ChemicalEntityOrGeneOrGeneProductǂbiolink:PhysicalEssenceǂbiolink:NamedThingǂbiolink:ChemicalEntityǂbiolink:MolecularEntityǂbiolink:SmallMoleculeǂbiolink:MolecularMixtureǂbiolink:ChemicalMixtureǂbiolink:PhysicalEssenceOrOccurrentǂbiolink:Drug

For xDTD refresh, we do the hard mapping (e.g., the preferred cure in old version maps to the preferred cure in new version) instead of normalized mapping (e.g., the preferred cure in old version maps to the equivalent curies in new version) because this can avoid the conflict mapping (e.g., one preferred cure in new version may have two or multiple embeddings in the old version because at least two of its equivalent curies are preferred cures in the old version). As such, for this case, when we refreshed the full version of v2.8.4 xDTD to v2.9.2 or v2.10.0, the PUBCHEM.COMPOUND:5754 doesn't appear anymore. Does this make sense?

I am now building the full version for v2.10.0. It should be resolved after that.

dkoslicki commented 1 month ago

Ah, I think I understand now. So this should be fixed after the xDTD rebuild for v2.10.0, right? In that case, I think we're good once that gets deployed

chunyuma commented 1 month ago

So this should be fixed after the xDTD rebuild for v2.10.0, right?

Yes, it is correct.

chunyuma commented 3 weeks ago

any idea why xDTD returns so few results in CI: https://arax.ci.transltr.io/?r=252131 (6 results from xDTD)

I ran a local test (see results below) on the same query graph using the new trained xDTD for KG2.10.0. Now it has more than 40 results. So, it seems like the new build of xDTD has fixed this issue.

[0, 'rituximab']
[1, 'siltuximab']
[2, 'cyclophosphamide']
[3, 'prednisone']
[4, 'dexamethasone acetate']
[5, 'methotrexate']
[6, 'bortezomib']
[7, '6alpha-methylprednisolone']
[8, 'cisplatin']
[9, 'gemcitabine']
[10, 'prenylamine']
[11, 'loracarbef']
[12, 'streptozocin']
[13, 'rabeprazole']
[14, 'mitomycin c']
[15, 'digoxin']
[16, 'capecitabine']
[17, 'prucalopride']
[18, 'tolmetin']
[19, 'imatinib']
[20, 'nateglinide']
[21, 'diethylstilbestrol']
[22, 'hexamethylmelamine']
[23, 'hydroxyurea']
[24, 'zoledronic acid']
[25, 'pantoprazole']
[26, 'idelalisib']
[27, 'tacrolimus (anhydrous)']
[28, 'temozolomide']
[29, 'captopril']
[30, 'imipramine']
[31, 'pamidronate']
[32, 'pemetrexed']
[33, 'alendronic acid']
[34, 'caplacizumab']
[35, 'actinomycin d']
[36, 'teniposide']
[37, 'tibolone']
[38, 'peginterferon alfa-2b']
[39, 'olaratumab']
[40, 'tiaprofenic acid']
[41, 'troglitazone']
[42, 'l-thyroxine']
[43, 'tacrine']
[44, 'propofol']
[45, 'oxatomide']
[46, 'lomustine']
[47, '2-[(4-ethynyl-2-fluorophenyl)amino]-3,4-difluoro-n-(2-hydroxyethoxy)benzamide']
[48, 'valganciclovir']
[49, 'melphalan']
dkoslicki commented 3 weeks ago

Let's keep this open until it's deployed to at least CI

chunyuma commented 2 weeks ago

Just verify we now have fixed this issue: https://arax.ci.transltr.io/?r=267094

So it is good to close this issue.