From 4d5fac8f9b42a56c5ca7d21dce3e9281fb9b2ec1 Mon Sep 17 00:00:00 2001 From: Robert Allaway Date: Thu, 26 Oct 2023 09:57:25 -0500 Subject: [PATCH] rename tool details tables this is to avoid collision of resourceType valid values and tool-type-components --- nf_research_tools.rdb.model.csv | 142 ++++++++++++++++---------------- 1 file changed, 71 insertions(+), 71 deletions(-) diff --git a/nf_research_tools.rdb.model.csv b/nf_research_tools.rdb.model.csv index 4dab9e14..32f86294 100644 --- a/nf_research_tools.rdb.model.csv +++ b/nf_research_tools.rdb.model.csv @@ -5,39 +5,39 @@ resourceId,A unique identifier for the resource.,,,TRUE,,resource,,, rrid,"The RRID, a standard resource identifier that will facilitate interoperability with other databases, and is an increasingly-used identifier for publications https://scicrunch.org/resources if available",,,FALSE,,resource,,, resourceName,The “canonical” name of the resource,,,TRUE,,resource,,, synonyms,Synonyms of the resource,,,FALSE,,resource,,,list like -resourceType,"Type of resource. (e.g. animal model, antibody, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, +resourceType,"Type of resource. (e.g. animal model, antibodyDetails, plasmid, etc.)","Animal Model, Cell Line, Antibody, Genetic Reagent, Biobank",,TRUE,,resource,,, description,Free text description/summary/overview/purpose of the resource.,,,FALSE,,resource,,, usageRequirements,Any known restrictions on use of the resource. ,"data sharing required, non-commercial use only, re-distribution not permitted, generation of germ line transmitting chimeras not permitted, creation of functional gametes not permitted, generation of interspecies chimeras not permitted, human cloning not permitted, cannot be used for treatment purposes, IRB documentation required, special licencing restrictions (see vendor for more information), unknown",,FALSE,,resource,,,list like howToAcquire,How to acquire a particular resource. ,,,TRUE,,resource,,, dateAdded,The date that the resource was originally added.,,,TRUE,,resource,,, dateModified,The last update of the resource metadata (not including observations).,,,TRUE,,resource,,, -geneticReagent,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagent,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, -geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagent,,, -insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagent,,, -insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagent,,, -gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagent,,, -insertSize,"Size, in bp, of the gene insert as it is in the plasmid.",,,FALSE,,geneticReagent,,, -insertSpecies,Species of the insert,"Homo sapiens, Mus musculus, Rattus norvegicus",,TRUE,,geneticReagent,,,list like -nTerminalTag,Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list like -cTerminalTag,Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagent,,,list like -cloningMethod,"How the vector was constructed. (e.g. restriction enzyme, TOPO cloning, etc.)","Restriction Enzyme, TOPO cloning, Gateway Cloning, Ligation Independent Cloning, Gibson Cloning, Unknown",,FALSE,,geneticReagent,,, -5primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 5' (N-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagent,,, -5primeSiteDestroyed,"If 5' site was destroyed during cloning. (e.g. yes, no, unknown).","Yes, No, Unknown",,FALSE,,geneticReagent,,, -3primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 3' (C-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagent,,, -3primeSiteDestroyed,"If 3' site was destroyed during cloning. (e.g. yes, no, unknown)","Yes, No, Unknown",,FALSE,,geneticReagent,,, -promoter,Promoter driving the expression of the insert in the plasmid,,,FALSE,,geneticReagent,,, -5primer,Primer to sequence the 5' end (N-terminal) of the insert,,,FALSE,,geneticReagent,,, -3primer,Primer to sequence the 3' end (C-terminal) of the insert.,,,FALSE,,geneticReagent,,, -vectorBackbone,Name of the backbone the plasmid is built on. (e.g pGBT9),,,FALSE,,geneticReagent,,, -vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Transposon Vector, Unspecified, Other",,FALSE,,geneticReagent,,,list like -backboneSize,Size in bp of the backbone without the insert,,,FALSE,,geneticReagent,,, -totalSize,Size of vector with insert. Derived from insertSize and backboneSize.,,,FALSE,,geneticReagent,,, -bacterialResistance,"Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)","Ampicillin, Kanamycin, Chloramphenicol, Tetracycline, Spectinomycin, Hygromycin, Bleocin(Zeocin), Gentamycin, Streptomycin, Nourseothricin(clonNat), Ampicillin and Bleocin (Zeocin), Ampicillin and Kanamycin, Ampicillin and Tetracycline, Ampicillin and Streptomycin, Ampicillin and Spectinomycin, Chloramphenicol and Ampicillin, Chloramphenicol and Bleocin (Zeocin), Chloramphenicol and Tetracycline, Chloramphenicol and Kanamycin, Chloramphenicol and Spectinomycin, Chloramphenicol and Gentamycin, Spectinomycin and Streptomycin, Other",,FALSE,,geneticReagent,,, -selectableMarker,"Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?","Neomycin, Puromycin, Hygromycin, Kanamycin, Chloramphenicol, Zeocin, Blasticidin, Gentamicin, TRP1, LEU1, LEU2, URA3, HIS3, Basta, Other",,FALSE,,geneticReagent,,, -copyNumber,"If a plasmid produces a sufficient amount of DNA from a normal miniprep or if plasmid requires special growth conditions or it is difficult to grow. (e.g. high copy, low copy, unknown).","High Copy, Low Copy, Unknown",,FALSE,,geneticReagent,,, -growthTemp,At what temperature should the bacteria hosting the plasmid be grown,"37 C, 30 C, Room Temperature",,FALSE,,geneticReagent,,, -growthStrain,"The E.Coli strain that should be used to distribute the plasmid. (e.g. DH5alpha, NEB Stable, etc.)","DH5alpha, DH10B, NEB Stable, ccdb Survival, Pir1, Other",,FALSE,,geneticReagent,,, -hazardous,"Does the unmodified plasmid DNA, either in purified form or when introduced into bacterial or mammalian cells require handling at Biosafety Level 2 or higher?","Yes, No, Unknown",,TRUE,,geneticReagent,,, +geneticReagentDetails,Genetic reagents.,,"Component, geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",FALSE,,geneticReagentDetails,"geneticReagentId, insertName, insertEntrezId, gRNAshRNASequence, insertSize, insertSpecies, nTerminalTag, cTerminalTag, cloningMethod, 5primeCloningSite, 5primeSiteDestroyed, 3primeCloningSite, 3primeSiteDestroyed, promoter, 5primer, 3primer, vectorBackbone, vectorType, backboneSize, totalSize, bacterialResistance, selectableMarker, copyNumber, growthTemp, growthStrain, hazardous",, +geneticReagentId,A unique identifier for the reagent.,,,TRUE,,geneticReagentDetails,,, +insertName,Name of the main gene insert in the plasmid.,,,TRUE,,geneticReagentDetails,,, +insertEntrezId,The entrez gene id for the gene insert,,,TRUE,,geneticReagentDetails,,, +gRNAshRNASequence,"The sequence of the gRNA or shRNA for the gene insert, if present. ",,,FALSE,,geneticReagentDetails,,, +insertSize,"Size, in bp, of the gene insert as it is in the plasmid.",,,FALSE,,geneticReagentDetails,,, +insertSpecies,Species of the insert,"Homo sapiens, Mus musculus, Rattus norvegicus",,TRUE,,geneticReagentDetails,,,list like +nTerminalTag,Any tags on the N terminal 5' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagentDetails,,,list like +cTerminalTag,Any tags on the C terminal 3' end of the gene insert in the plasmid. Only tags that are in frame,,,FALSE,,geneticReagentDetails,,,list like +cloningMethod,"How the vector was constructed. (e.g. restriction enzyme, TOPO cloning, etc.)","Restriction Enzyme, TOPO cloning, Gateway Cloning, Ligation Independent Cloning, Gibson Cloning, Unknown",,FALSE,,geneticReagentDetails,,, +5primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 5' (N-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagentDetails,,, +5primeSiteDestroyed,"If 5' site was destroyed during cloning. (e.g. yes, no, unknown).","Yes, No, Unknown",,FALSE,,geneticReagentDetails,,, +3primeCloningSite,"If Restriction Enzyme was selected as the cloning method, specifies what enzyme was used on the 3' (C-terminal) end of the insert",,cloningMethod,FALSE,,geneticReagentDetails,,, +3primeSiteDestroyed,"If 3' site was destroyed during cloning. (e.g. yes, no, unknown)","Yes, No, Unknown",,FALSE,,geneticReagentDetails,,, +promoter,Promoter driving the expression of the insert in the plasmid,,,FALSE,,geneticReagentDetails,,, +5primer,Primer to sequence the 5' end (N-terminal) of the insert,,,FALSE,,geneticReagentDetails,,, +3primer,Primer to sequence the 3' end (C-terminal) of the insert.,,,FALSE,,geneticReagentDetails,,, +vectorBackbone,Name of the backbone the plasmid is built on. (e.g pGBT9),,,FALSE,,geneticReagentDetails,,, +vectorType,"Primary function of the plasmid. (e.g. mammalian expression, bacterial expression, etc.)","Mammalian Expression, Bacterial Expression, Gateway Entry Clone, Lentiviral, Adenoviral, AAV, RNAi, Luciferase, Cre/Lox, Yeast Expression, Worm Expression, Insect Expression, Plant Expression, Mouse Targeting, CRISPR, TALEN, Synthetic Biology, Transfer Vector, Transposon Vector, Unspecified, Other",,FALSE,,geneticReagentDetails,,,list like +backboneSize,Size in bp of the backbone without the insert,,,FALSE,,geneticReagentDetails,,, +totalSize,Size of vector with insert. Derived from insertSize and backboneSize.,,,FALSE,,geneticReagentDetails,,, +bacterialResistance,"Antibiotic(s) that should be used for selection in bacteria. (e.g. ampicillin, kanamycin, etc.)","Ampicillin, Kanamycin, Chloramphenicol, Tetracycline, Spectinomycin, Hygromycin, Bleocin(Zeocin), Gentamycin, Streptomycin, Nourseothricin(clonNat), Ampicillin and Bleocin (Zeocin), Ampicillin and Kanamycin, Ampicillin and Tetracycline, Ampicillin and Streptomycin, Ampicillin and Spectinomycin, Chloramphenicol and Ampicillin, Chloramphenicol and Bleocin (Zeocin), Chloramphenicol and Tetracycline, Chloramphenicol and Kanamycin, Chloramphenicol and Spectinomycin, Chloramphenicol and Gentamycin, Spectinomycin and Streptomycin, Other",,FALSE,,geneticReagentDetails,,, +selectableMarker,"Are there any additional selection markers on this plasmid, for example, any mammalian selection markers or fluorescent proteins?","Neomycin, Puromycin, Hygromycin, Kanamycin, Chloramphenicol, Zeocin, Blasticidin, Gentamicin, TRP1, LEU1, LEU2, URA3, HIS3, Basta, Other",,FALSE,,geneticReagentDetails,,, +copyNumber,"If a plasmid produces a sufficient amount of DNA from a normal miniprep or if plasmid requires special growth conditions or it is difficult to grow. (e.g. high copy, low copy, unknown).","High Copy, Low Copy, Unknown",,FALSE,,geneticReagentDetails,,, +growthTemp,At what temperature should the bacteria hosting the plasmid be grown,"37 C, 30 C, Room Temperature",,FALSE,,geneticReagentDetails,,, +growthStrain,"The E.Coli strain that should be used to distribute the plasmid. (e.g. DH5alpha, NEB Stable, etc.)","DH5alpha, DH10B, NEB Stable, ccdb Survival, Pir1, Other",,FALSE,,geneticReagentDetails,,, +hazardous,"Does the unmodified plasmid DNA, either in purified form or when introduced into bacterial or mammalian cells require handling at Biosafety Level 2 or higher?","Yes, No, Unknown",,TRUE,,geneticReagentDetails,,, vendorItem,The resource item associated with a vendor.,,"Component, vendorItemId, vendorId, resourceId, catalogNumber, catalogNumberURL",FALSE,,vendorItem,"vendorItemId, vendorId, resourceId, catalogNumber, catalogNumberURL","resource,vendor", vendorItemId,A unique identifier for the resource associated with a vendor. ,,,TRUE,,vendorItem,,, catalogNumber,The catalog number associated with the resource pertaining to the vendor that sells the resource.,,,TRUE,,vendorItem,,, @@ -46,16 +46,16 @@ vendor,A person or compnay offering the resource for sale.,,"Component, vendorId vendorId,A unique identifier for the vendor.,,,TRUE,,vendor,,, vendorName,The name of the vendor.,,,FALSE,,vendor,,, vendorURL,The vendor website url associated with the resource.,,,FALSE,,vendor,,, -biobank,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobank,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, -biobankName,The name of the biobank. ,,,TRUE,,biobank,,, -biobankId,A unique identifier for the biobank.,,,TRUE,,biobank,,, -biobankURL,A URL for the biobank landing page.,,,TRUE,,biobank,,, -specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobank,,,list like -specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobank,,,list like -tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobank,,,list like -diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobank,,,list like -specimenPreparationMethod,The preservation methods used by the biobank.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobank,,,list like -specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobank,,,list like +biobankDetails,"A large collection of biological or medical data and tissue samples, amassed for research purposes.",,"Component, biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",FALSE,,biobankDetails,"biobankId, resourceId, biobankName, biobankURL, specimenType, specimenTissueType, tumorType, diseaseType, specimenPreparationMethod, specimenFormat",, +biobankName,The name of the biobankDetails. ,,,TRUE,,biobankDetails,,, +biobankId,A unique identifier for the biobankDetails.,,,TRUE,,biobankDetails,,, +biobankURL,A URL for the biobankDetails landing page.,,,TRUE,,biobankDetails,,, +specimenType,The types of specimens that are banked.,"human tissue, xenograft tumors, cell lines",,TRUE,,biobankDetails,,,list like +specimenTissueType,The types of tissues that are banked.,"blood, tumor, cerebrospinal fluid, nerve, skin, bone, brain",,TRUE,,biobankDetails,,,list like +tumorType,"The types of tumors that are banked, if applicable.","cutaneous neurofibroma, plexiform neurofibroma, schwannoma, meningioma, malignant peripheral nerve sheath tumor, low grade glioma, high grade glioma, pheochromocytoma, optic nerve glioma, atypical neurofibroma, neurofibroma NOS, diffuse infiltrating neurofibroma, brain NOS",,TRUE,,biobankDetails,,,list like +diseaseType,"The diseases of the banked specimens, if applicable.","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis",,TRUE,,biobankDetails,,,list like +specimenPreparationMethod,The preservation methods used by the biobankDetails.,"Fresh collected, Flash frozen, FFPE, Cryopreserved, OCT, RNA later, Formalin-fixed, Ethanol",,TRUE,,biobankDetails,,,list like +specimenFormat,How the specimens have been processed in preparation for distribution.,"whole tumor, slide, whole cell lysate, DNA, RNA",,TRUE,,biobankDetails,,,list like observation,"A remark, statement, or comment based on the resource.",,"Component, observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink",FALSE,,observation,"observationId, resourceId, publicationId, observationSubmitterName, synapseId, observationText, observationType, observationPhase, observationTime, observationTimeUnits, reliabilityRating, easeOfUseRating, observationLink","resource, investigator, publication", observationId,A unique identifier for the observation.,,,TRUE,,observation,,, observationSubmitterName,The name of the person submitting the observation. ,,,TRUE,,observation,,, @@ -73,15 +73,15 @@ resourceApplicationId,A unique identifier for resrouce Application,,,TRUE,,resou source,"The source of resource application information (e.g. Vendor, Community)","Community-reported, Investigator-reported, Vendor-reported",,TRUE,,resourceApplication,,, applications,"One or more uses for the resource (e.g. western blot, immunofluorescence)","Western Blot, Immunofluorescence, ELISA, Immunohistochemistry, Immunoprecipitation, Tumor Growth Studies, Immunohistochemistry (Paraffin-Embedded), Immunocytochemistry, Immunohistochemistry (Frozen Sections), Flow Cytometry, Affinity Purification, Microarray",,TRUE,,resourceApplication,,,list like links,shareable links related to the resource,,,FALSE,,resourceApplication,,,list -antibody,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibody,,, -antibodyId,A unique identifier for the antibody.,,,TRUE,,antibody,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, -uniprotId,The uniprotId of the antibody.,,,TRUE,,antibody,,, -targetAntigen,Antigen that is targeted by antibody. (e.g. Neurofibromin 1 human),,,TRUE,,antibody,,, -clonality,They type of clonality of the antibody,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibody,,, -cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibody,,, -reactiveSpecies,Species the antibody has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibody,,,list -conjugate,Is the antibody conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibody,,, -hostOrganism,The species of the organism that hosts the antibody,"Mouse, Rabbit",,TRUE,,antibody,,, +antibodyDetails,"A blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as bacteria, viruses, and foreign substances in the blood.",,"Component, antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",FALSE,,antibodyDetails,,, +antibodyId,A unique identifier for the antibodyDetails.,,,TRUE,,antibodyDetails,"antibodyId, uniprotId, targetAntigen, clonality, cloneId, reactiveSpecies, conjugate, hostOrganism",, +uniprotId,The uniprotId of the antibodyDetails.,,,TRUE,,antibodyDetails,,, +targetAntigen,Antigen that is targeted by antibodyDetails. (e.g. Neurofibromin 1 human),,,TRUE,,antibodyDetails,,, +clonality,They type of clonality of the antibodyDetails,"Unknown, Cocktail, Control, Isotype Control, Monoclonal, Monoclonal Secondary, Polyclonal, Polyclonal Secondary, OligoClonal, Recombinant, Recombinant Monoclonal, Recombinant Monoclonal Secondary, Recombinant Polyclonal, Recombinant Polyclonal Secondary",,TRUE,,antibodyDetails,,, +cloneId,Identification of clone (e.g. 2D1),,,FALSE,,antibodyDetails,,, +reactiveSpecies,Species the antibodyDetails has been shown to crossreact with the target protein. ,"Avian, Bovine, Canine, Chicken, Cow, Dog, Donkey, Feline, Fish, Guinea pig, Hamster, Human, Monkey, Mouse, Non-human primate, Other, Pig, Porcine, Rabbit, Rat, Rodent, Sheep, Simian, Zebrafish",,TRUE,,antibodyDetails,,,list +conjugate,Is the antibodyDetails conjugated or nonconjugated,"Conjugated, Nonconjugated",,TRUE,,antibodyDetails,,, +hostOrganism,The species of the organism that hosts the antibodyDetails,"Mouse, Rabbit",,TRUE,,antibodyDetails,,, donor,"A person, animal, etc. who is the contributor of the resource.",,"Component, donorId, parentDonorId, transplantationDonorId, species, sex, age, race",FALSE,,donor,"donorId, parentDonorId, transplantationDonorId, species, sex, age, race",, donorId,A uniqe identifier for donor.,,,TRUE,,donor,,, parentDonorId,The ID of the parent donor.,,donorId,FALSE,,donor,,, @@ -89,18 +89,18 @@ species,The species of the individual the resource was derived from.,"Homo sapie sex,The sex of the individual from which the resource was derived from.,"Male, Female, Unknown",,FALSE,,donor,,, age,That age of the individual from which the resource was derived from.,,,FALSE,,donor,,, race,The ethnicity of the individual the resource was derived from.,,,FALSE,,donor,,, -cellLine,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLine,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, -cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLine,,, -organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLine,,, -tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLine,,, -cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLine,,, -originYear,The year the cell line orginated.,,,FALSE,,cellLine,,, -strProfile,Short tandem repeat profile information.,,,FALSE,,cellLine,,, -populationDoublingTime,Time for cell line to double,,,FALSE,,cellLine,,, -resistance,List of compounds if a cell line has been selected for.,,,FALSE,,cellLine,,,list -contaminatedMisidentified,If a cell line has been contaminated or misidentified,,,FALSE,,cellLine,,, -cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLine,,,list -cellLineManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)",,,FALSE,,cellLine,,,list +cellLineDetails,A cell culture selected for uniformity from a cell population derived from a usually homogeneous tissue source (such as an organ).,,"Component, cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",FALSE,,cellLineDetails,"cellLineId, donorId, organ, tissue, cellLineCategory, originYear, strProfile, populationDoublingTime, resistance, contaminatedMisidentified, cellLineGeneticDisorder, cellLineManifestation",donor, +cellLineId,A unique identifier for the cell line.,,,TRUE,,cellLineDetails,,, +organ,The organ the cell line is derived from.,"Biliary Tract, Bladder, Bone Marrow, Brain, Breast, Bronchial Tree, Duct, Epididymis, Esophagus, Fallopian Tube, Gallbladder, Gland, Gonad, Heart, Intestine, Kidney, Liver, Lung, Lymph Node, Ear, Eye, Nose, Tongue, Pancreas, Penis, Seminal Vesicle, Skin, Spermatic Cord, Spinal Cord, Spleen, Stomach, Thymus Gland, Tonsil, Trachea, Tracheobronchial Tree, Ureter, Urethra, Uterus, Vagina, Vulva",,FALSE,,cellLineDetails,,, +tissue,The tissue the cell line is derived from.,"Blood, Bone marrow, Buccal mucosa, Buffy coat, Cerebral cortex, Dorsal root ganglion, Embryonic tissue, Meninges, Nerve tissue, Optic nerve, Plasma, Primary tumor, Sciatic nerve, Serum, Splenocyte, Unspecified, Whole brain",,FALSE,,cellLineDetails,,, +cellLineCategory,The category to which the cell line belongs.,"Cancer cell line, Conditionally immortalized cell line, Embryonic stem cell, Factor-dependent cell line, Finite cell line, Hybridoma, Induced pluripotent stem cell, Somatic stem cell, Spontaneously immortalized cell line, Stromal cell line, Telomerase immortalized cell line, Transformed cell line, Undefined cell line type",,FALSE,,cellLineDetails,,, +originYear,The year the cell line orginated.,,,FALSE,,cellLineDetails,,, +strProfile,Short tandem repeat profile information.,,,FALSE,,cellLineDetails,,, +populationDoublingTime,Time for cell line to double,,,FALSE,,cellLineDetails,,, +resistance,List of compounds if a cell line has been selected for.,,,FALSE,,cellLineDetails,,,list +contaminatedMisidentified,If a cell line has been contaminated or misidentified,,,FALSE,,cellLineDetails,,, +cellLineGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,FALSE,http://purl.obolibrary.org/obo/NCIT_C3101,cellLineDetails,,,list +cellLineManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.)",,,FALSE,,cellLineDetails,,,list mutationDetails,"The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations",,"Component, mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",FALSE,,mutationDetails,"mutationDetailsId, externalMutationID, alleleType, mutationType, mutationMethod, affectedGeneSymbol, affectedGeneName, sequenceVariation, proteinVariation, animalModelMutation, humanClinVarMutation, chromosome",, mutationDetailsId,A unique identifier for mutation.,,,FALSE,,mutationDetails,,, externalMutationID,"An identifier from an organism database such as MGI or other curated variant resource, if available. ",,,FALSE,,mutationDetails,,, @@ -114,19 +114,19 @@ proteinVariation,The protein consequence of the mutation described in sequence v animalModelMutation,"A description of the specific mutation(s) created in the genome. (e.g. A neomycin resistance cassette replaced the first 42 codons of exon 31, the exon 31 splice acceptor site, and approximately 2 kb of intron 30.)",,,FALSE,,mutationDetails,,, humanClinVarMutation,"The human equivalent, of the mutation being described in ClinVar/HGVS notation. Can be used to link animal model mutations to the mutation they are modeling in human disease. ",,,FALSE,,mutationDetails,,, chromosome,Chromosome number of affected gene. (e.g. 11),,,FALSE,,mutationDetails,,, -mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModel, cellLine", +mutation,(intermediary table),,"Component, mutationId, mutationDetailsId, animalModelId, cellLineId",FALSE,,mutation,"mutationId, mutationDetailsId, animalModelId, cellLineId","mutationDetails, animalModelDetails, cellLineDetails", mutationId,A unique identifier for the mutation burden of the resource.,,,FALSE,,mutation,,, -animalModel,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModel,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, -animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModel,,, -animalState,"State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)",,,FALSE,,animalModel,,, -backgroundStrain,"An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.",,,FALSE,,animalModel,,, -backgroundSubstrain,"The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ",,,FALSE,Sage Bionetworks,animalModel,,, -strainNomenclature,The standard nomenclature for the strain. (e.g. B6.129S2-NF1tm1Tyj/J). Set by the International Committee on Standardized Genetic Nomenclature for Mice. See http://www.informatics.jax.org/mgihome/nomen/strains.shtml for nomenclature information.,,,FALSE,http://www.informatics.jax.org/mgihome/nomen/strains.shtml,animalModel,,, -generation,The generation of the animal model. (e.g. 13),,,FALSE,,animalModel,,, -transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,animalModel,,, -transplantationDonorId,The donor indentifier number for the transplantion donor. ,,donorId,FALSE,,animalModel,,, -animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModel,,,list -animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModel,,,list +animalModelDetails,"An animal sufficiently like humans in its anatomy, physiology, or response to a pathogen to be used in medical research in order to obtain results that can be extrapolated to human medicine.",,"Component, animalModelId, donorId, transplantationDonorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, animalModelGeneticDisorder, animalModelOfManifestation",FALSE,,animalModelDetails,"animalModelId, donorId, animalState, backgroundStrain, backgroundSubstrain, strainNomenclature, generation, transplantationType, transplantationDonorId, animalModelGeneticDisorder, animalModelOfManifestation",donor, +animalModelId,A unique identifier for the animal model.,,,TRUE,,animalModelDetails,,, +animalState,"State the animal is in according to the vendor/developer. (e.g. embryo, sperm, live)",,,FALSE,,animalModelDetails,,, +backgroundStrain,"An assigned name that describes the genetic make-up (all its alleles at all loci) except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. Correct strain nomenclature indicates what a mutant strain’s background is.",,,FALSE,,animalModelDetails,,, +backgroundSubstrain,"The substrain is a particular variety of a strain. For example, a C57BL/6 mice may have a substrain of C57BL/6J, C57BL/6Tac, or another substrain. ",,,FALSE,Sage Bionetworks,animalModelDetails,,, +strainNomenclature,The standard nomenclature for the strain. (e.g. B6.129S2-NF1tm1Tyj/J). Set by the International Committee on Standardized Genetic Nomenclature for Mice. See http://www.informatics.jax.org/mgihome/nomen/strains.shtml for nomenclature information.,,,FALSE,http://www.informatics.jax.org/mgihome/nomen/strains.shtml,animalModelDetails,,, +generation,The generation of the animal model. (e.g. 13),,,FALSE,,animalModelDetails,,, +transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,animalModelDetails,,, +transplantationDonorId,The donor indentifier number for the transplantion donor. ,,donorId,FALSE,,animalModelDetails,,, +animalModelGeneticDisorder,"Genetic diseases are diseases in which inherited genes predispose to increased risk. The genetic disorders associated with cancer often result from an alteration or mutation in a single gene. The diseases range from rare dominant cancer family syndrome to familial tendencies in which low-penetrance genes may interact with other genes or environmental factors to induce cancer. Research may involve clinical, epidemiologic, and laboratory studies of persons, families, and populations at high risk of these disorders. [ NCI ]","Neurofibromatosis type 1, Neurofibromatosis type 2, Schwannomatosis, No known disease",,TRUE,http://purl.obolibrary.org/obo/NCIT_C3101,animalModelDetails,,,list +animalModelOfManifestation,"Manifestations/symptoms that this resource is used to model (e.g. tumor type, behavioral phenotype, etc.) ",,,TRUE,,animalModelDetails,,,list development,"resourceId, investigatorId, publicationId, funderId (intermediary table)",,"Component, developmentId, resourceId, investigatorId, publicationId, funderId",FALSE,,development,"developmentId, resourceId, investigatorId, publicationId, funderId","resource, investigator, publication, funder", developmentId,A unique identifier for the development of the resource.,,,TRUE,,development,,, funder,A person or organization that provides money for a particular resource.,,"Component, funderId, funderName",FALSE,,funder,"funderId, funderName",,