From 481492e2a271ee13f894eeb885869bf0d013803b Mon Sep 17 00:00:00 2001 From: Adam Taylor Date: Thu, 30 May 2024 14:00:48 +0100 Subject: [PATCH 1/2] Update HTAN.model.csv --- HTAN.model.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HTAN.model.csv b/HTAN.model.csv index e60ec5af..199fcf75 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -455,7 +455,7 @@ Acquisition Method Type,Records the method of acquisition or source for the spec Other Acquisition Method,A custom acquisition method,,Acquisition Method Other Specify,,FALSE,Biospecimen,,, Acquisition Method Other Specify,A custom acquisition method [Text - max length 100 characters],,,,TRUE,Biospecimen,,, Preservation Method,Text term that represents the method used to preserve the sample.,"Cryopreserved, Cryopreservation in liquid nitrogen - dead tissue, Cryopreservation in dry ice - dead tissue, Cryopreservation in liquid nitrogen - live cells, Formalin fixed paraffin embedded - FFPE, Formalin fixed-unbuffered, Formalin fixed-buffered, Fresh, Fresh dissociated and single cell sorted into plates in NP40 buffer, OCT, Snap Frozen, Frozen, Negative 80 Deg C, Liquid Nitrogen, Fresh dissociated, Fresh dissociated and single cell sorted, Fresh dissociated and single cell sorted into plates, Methacarn fixed paraffin embedded - MFPE, unknown, Not Reported",,,TRUE,Biospecimen,,, -Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Carnoy's Fixative, Polaxamer, Other, None, unknown",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=65078&version=3.0, +Fixative Type,Text term to identify the type of fixative used to preserve a tissue specimen,"Acetone, Alcohol, Formalin, Glutaraldehyde, OCT media, RNAlater, Saline, 95% Ethanol, Dimidoester, Carbodiimide, Dimethylacetamide, Para-benzoquinone, PAXgene tissue, TCL lysis buffer, NP40 lysis buffer, Methacarn, Cryo-store, Carnoy's Fixative, Polaxamer, Other, None, unknown, Unfixed",,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=65078&version=3.0, Fixation Duration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",,,,TRUE,Biospecimen,,https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=5230144&version=1.0, Ischemic Time,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",,,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description, Ischemic Temperature,Specify whether specimen experienced warm or cold ischemia.,"Warm Ischemia, Cold Ischemia, Ambient air, 4C wet ice, Negative -20C, Dry Ice, Liquid Nitrogen, unknown",,,FALSE,Biospecimen,,https://data.humancellatlas.org/metadata/dictionary/biomaterial/specimen_from_organism#specimen_from_organism-state_of_specimen-gross_description, From 4a6bfe99b020bcb192f98b394ebc92b2b801b0f3 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 30 May 2024 13:08:13 +0000 Subject: [PATCH 2/2] GitHub Action: convert *.model.csv to *.model.jsonld --- HTAN.model.jsonld | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index de8bd16b..a6c0841c 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -27693,6 +27693,9 @@ }, { "@id": "bts:Unknown" + }, + { + "@id": "bts:Unfixed" } ], "sms:displayName": "Fixative Type", @@ -57110,6 +57113,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Unfixed", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Unfixed", + "rdfs:subClassOf": [ + { + "@id": "bts:FixativeType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Unfixed", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:WarmIschemia", "@type": "rdfs:Class",