Merge pull request #65 from eliteportal/LC-mice-organ-and-tissue-vali…

…d-values

added LC tissue and organ valid valuess

EL.data.model.csv

@@ -176,10 +176,10 @@ cellType,Indicate the cell type.,"A549, arachnoid, astrocytes, B-lymphocytes, CD
 fastingState,Was individual fasting when the sample was taken (true/false)?,"FALSE,Not applicable,Not collected,Not specified,TRUE,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.fastingState-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human"
 isPostMortem,Was the sample taken after death (true/false)?,"TRUE, FALSE",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.isPostMortem-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human"
 nucleicAcidSource,"Specifies the type of nucleic acid (DNA, RNA, Pooled, etc.) found in a sample.","bulk cell,bulk nuclei,mitochondria,Not applicable,Not collected,Not specified,single cell,single nucleus,sorted cells,sorted nuclei,Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-ngs.nucleicAcidSource-0.0.3,biospecimen,False,STRING,https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=23.04d&ns=ncit&code=C171278&key=1146649015&b=1&n=1, ,"Biospecimen_human,Biospecimen_non_Human"
-organ,Indicate the organ the specimen is from,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.organ-0.0.4,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C13018, ,"Biospecimen_human,Biospecimen_non_Human"
+organ,Indicate the organ the specimen is from,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown, plasma, gonadal fat, inguinal fat, gastrocnemius muscle",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.organ-0.0.4,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C13018, ,"Biospecimen_human,Biospecimen_non_Human"
 samplingAge,"The calculated age of the sample, measurement is determined or coded by the data contributor.Other,Unknown, Not collected, Not applicable",,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.samplingAge-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human"
 specimenID,"Identifying string linked to a particular sample or specimen, provide by the data contributor",,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.specimenID-0.0.2,biospecimen,False,STRING,Sage Bionetworks,n/a (unique to each data contributor). ,"Biospecimen_human,Biospecimen_non_Human,Genotyping_Human,Metabolomics,Metagenomics,Microbiome,Proteomics,RNAseq,Whole_Genome_Sequencing,bsSeq,scRNAseq"
-tissue,Indicate the tissue the specimen is from,"amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.tissue-0.0.11,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C12801, ,"Biospecimen_human,Biospecimen_non_Human"
+tissue,Indicate the tissue the specimen is from,"amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain, gonadal fat, inguinal fat, kidney, plasma, liver, gastrocnemius muscle",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.tissue-0.0.11,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C12801, ,"Biospecimen_human,Biospecimen_non_Human"
 tissueWeight,The mass of the tissue specimen. Measured in mg.,,,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.tissueWeight-0.0.2,biospecimen,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human"
 diagnosis,Indicate the disease or condition.,"AD-DS, Affective Disorder, Alzheimer Disease, Alzheimer disease with psychosis, amyotrophic lateral sclerosis, anxiety, Autism Spectrum Disorder, Bipolar Disorder, Bladder Cancer, Brain Cancer, Breast Cancer, Cervical Cancer, Colon Cancer, control, corticobasal degeneration disorder, CS-DS, dementia, dystonia, essential tremor, Fibrocystic Breast Disease, frontotemporal dementia, gliosis, hypoxia, Juvenile Myelomonocytic Leukemia, Leukemia, Lewy body disease, Longevity, Lung Cancer, Major Depressive Disorder, MCI-DS, mild cognitive impairment, multiple system atrophy, Neurofibromatosis 1, Neurofibromatosis 2, no cognitive impairment, Not Applicable, obesity, obsessive compulsive disorder, Ovary Cancer, Pancreatic Cancer, Parkinson's disease, pathological aging, progressive supranuclear palsy, Prostate Cancer, Schizophrenia, Skin Cancer, Substance Related Disorder, Tourette Syndrome, traumatic brain injury, type 2 diabetes mellitus, vascular dementia, Williams Syndrome",,,False,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.diagnosis-0.0.12,clinical,True,STRING,"https://www.ebi.ac.uk/ols/ontologies/mondo, https://www.ebi.ac.uk/ols/ontologies/maxo, https://www.ebi.ac.uk/ols/ontologies/hp","HPO, MONDO, MAXO codes or labels (not listed for purposes of this RFC), Other, Unknown, Not collected, Not applicable, Not specified. ","Individual_Human,Phenotype_human"
 ethnicity,Ethnicity of individual,"Hispanic or Latino,Not Hispanic or Latino,Prefer not to answer,Not Applicable",,,True,ManifestColumn,,ManifestColumn,sage.annotations-demographics.ethnicity-0.0.2,demographics,False,STRING,"Sage Bionetworks, https://www.synapse.org/#!Synapse:syn25878249", ,"Individual_Human,Phenotype_human"

EL.data.model.jsonld

@@ -6908,6 +6908,9 @@
                 {
                     "@id": "bts:SpecimenType"
                 },
+                {
+                    "@id": "bts:Organ"
+                },
                 {
                     "@id": "bts:Tissue"
                 }
@@ -7290,6 +7293,18 @@
                 },
                 {
                     "@id": "bts:Wholebrain"
+                },
+                {
+                    "@id": "bts:Gonadalfat"
+                },
+                {
+                    "@id": "bts:Inguinalfat"
+                },
+                {
+                    "@id": "bts:Kidney"
+                },
+                {
+                    "@id": "bts:Gastrocnemiusmuscle"
                 }
             ],
             "sms:displayName": "tissue",
@@ -10152,6 +10167,18 @@
                 },
                 {
                     "@id": "bts:Unknown"
+                },
+                {
+                    "@id": "bts:Plasma"
+                },
+                {
+                    "@id": "bts:Gonadalfat"
+                },
+                {
+                    "@id": "bts:Inguinalfat"
+                },
+                {
+                    "@id": "bts:Gastrocnemiusmuscle"
                 }
             ],
             "sms:displayName": "organ",
@@ -10271,6 +10298,9 @@
             "rdfs:subClassOf": [
                 {
                     "@id": "bts:Organ"
+                },
+                {
+                    "@id": "bts:Tissue"
                 }
             ],
             "schema:isPartOf": {
@@ -10487,6 +10517,66 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Gonadalfat",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Gonadalfat",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Organ"
+                },
+                {
+                    "@id": "bts:Tissue"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "gonadal fat",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Inguinalfat",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Inguinalfat",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Organ"
+                },
+                {
+                    "@id": "bts:Tissue"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "inguinal fat",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Gastrocnemiusmuscle",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "TBD",
+            "rdfs:label": "Gastrocnemiusmuscle",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Organ"
+                },
+                {
+                    "@id": "bts:Tissue"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "gastrocnemius muscle",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:SamplingAge",
             "@type": "rdfs:Class",

modules/biospecimen/organ.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-organ,Indicate the organ the specimen is from,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.organ-0.0.4,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C13018, ,"Biospecimen_human,Biospecimen_non_Human"
+organ,Indicate the organ the specimen is from,"blood, bone marrow, brain, breast, Bursa Of Fabricius, cerebrospinal fluid, colon, kidney, large intestine, liver, lung, lymph node, mammary gland, nerves, nose, ovary, pancreas, prostate, skin, spleen, Not collected, Not specified, Not applicable, Other, Unknown, plasma, gonadal fat, inguinal fat, gastrocnemius muscle",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.organ-0.0.4,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C13018, ,"Biospecimen_human,Biospecimen_non_Human"

modules/biospecimen/tissue.csv

@@ -1,2 +1,2 @@
 Attribute,Description,Valid Values,DependsOn,DependsOn Component,Required,Parent,Validation Rules,Properties,Source,module,multivalue,columnType,Ontology,Notes,UsedIn
-tissue,Indicate the tissue the specimen is from,"amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.tissue-0.0.11,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C12801, ,"Biospecimen_human,Biospecimen_non_Human"
+tissue,Indicate the tissue the specimen is from,"amygdala, amygdaloid complex, anterior cingulate cortex, angular gyrus, blood, bone marrow, Buccal Mucosa, Buffy Coat, caudate nucleus, cecum derived fecal material, cerebellar cortex, cerebellum, cerebral cortex, cortical plate, dorsal anterior cingulate cortex, dorsal pallium, Dorsal Root Ganglion, dorsolateral prefrontal cortex, dorsomedial prefrontal cortex, embryonic tissue, entorhinal cortex, fecal material, forebrain, frontal cortex, frontal lobe, frontal pole, fusiform gyrus, hippocampus, head of caudate nucleus, inferior frontal gyrus, inferior temporal cortex, inferior temporal gyrus, inferolateral temporal cortex, insula, insular cortex, lateral entorhinal cortex, left cerebral hemisphere, liver, mammillary body, medial dorsal nucleus of thalamus, medial entorhinal cortex, medial frontal cortex, medial ganglionic eminence, medial orbital frontal cortex, medial prefrontal cortex, meninges, midbrain, middle frontal gyrus, middle temporal gyrus, nerve tissue, Not Applicable, nucleus accumbens, occipital lobe, occipital visual cortex, olfactory neuroepithelium, orbitofrontal cortex, parahippocampal gyrus, parietal cortex, parietal lobe, plasma, posterior cingulate cortex, posteroinferior parietal cortex, posterior inferior parietal cortex, posterior superior temporal cortex, precentral gyrus, prefrontal cortex, primary auditory cortex, primary motor cortex, primary somatosensory cortex, primary tumor, primary visual cortex, putamen, right cerebral hemisphere, serum, splenocyte, striatum, subgenual anterior cingulate cortex, subgenual cingulate cortex, superior parietal lobe, superior temporal gyrus, temporal cortex, temporal lobe, temporal pole, thalamus, unspecified, ventricular zone, ventrolateral prefrontal cortex, VZ/SVZ, whole brain, gonadal fat, inguinal fat, kidney, plasma, liver, gastrocnemius muscle",,,True,ManifestColumn,,ManifestColumn,sage.annotations-experimentalData.tissue-0.0.11,biospecimen,False,STRING,http://purl.obolibrary.org/obo/NCIT_C12801, ,"Biospecimen_human,Biospecimen_non_Human"