update data model csv and convert to jsonld

Author: melissarklein

EL.data.model.csv

@@ -118,8 +118,8 @@ sequencingBatchSizeUnit,The unit of measurement for number of samples in a batch
 sop,"Relevant standard operating procedures. Standard operating procedures used in the assembly and/or annotation of genomes, metagenomes, or environmental sequences. Example - 'http-//press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/)'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics
 sourceMatID,"Source material identifiers. A unique identifier assigned to a material sample (as defined by http-//rs.tdwg.org/dwc/terms/materialSampleID and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing.The identifier can refer to the original material collected or any derived sub-samples. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,MIMS (Minimum information about a metagenome sequence., https://pubmed.ncbi.nlm.nih.gov/18479204/,Metagenomics
 speciesAge,"Age of individual (formatted in months, ex. ""72 months"").note- Uncertainty about the age might require recording age by specifying a lower and upper estimate in months for the age of the animal.",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,"Sage Bionetworks, https://www.animalaudiograms.org/audiogram_metadata_scheme#:~:text=species%20are%20possible.-,age,-The%20age%20of", ,Individual_non_Human
-speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,"Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C62690https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045, ,"Individual_non_Human,Phenotype_human"
-speciesName,"The scientific name of the species (typically a taxonomic group, ex. ""Eremophila alpestris) the individual belongs to.""""""","Multi-species,Not applicable,Not collected,Not specified,Unknown",,,True,ManifestColumn,allowOther,ManifestColumn,,ManifestColumn,False,STRING,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045,example: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135430. ,Individual_non_Human
+speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,"Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C62690https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045, ,"file_annotation_template,Individual_non_Human,Phenotype_human"
+speciesName,"The scientific name of the species (typically a taxonomic group, ex. ""Eremophila alpestris) the individual belongs to.""""""",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_1045,example: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135430. ,"file_annotation_template,Individual_non_Human"
 specimenAge,"The subject's age at the time of specimen extraction is the individual's age (since birth) at the time a given specimen was extracted. Measured as age in years. Other, Unknown, Not collected, Not applicable",,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,Sage Bionetworks, ,"Biospecimen_human,Biospecimen_non_Human"
 specimenSource,Indicate the biological area of the specimen,,,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,False,STRING,https://www.ebi.ac.uk/ols/ontologies/ccf/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0004537&lang=en&viewMode=PreferredRoots&siblings=false, ,"Biospecimen_human,Biospecimen_non_Human"
 specimenType,Type of biological material comprising the Specimen,"blood,Cerebrospinal Fluid (CSF),Not applicable,Not collected,Not specified,organoid,plasma,saliva,serum,sputum,stool,swabs,tissue,Unknown,urine",,,True,ManifestColumn,,ManifestColumn,,ManifestColumn,True,STRING,"Sage Bionetworks, http://purl.obolibrary.org/obo/NCIT_C70713", ,"Biospecimen_human,Biospecimen_non_Human"

EL.data.model.jsonld

@@ -2632,9 +2632,6 @@
                 {
                     "@id": "bts:RunType"
                 },
-                {
-                    "@id": "bts:SpeciesName"
-                },
                 {
                     "@id": "bts:Stage"
                 },
@@ -2733,9 +2730,6 @@
                 {
                     "@id": "bts:MsTarget"
                 },
-                {
-                    "@id": "bts:SpeciesName"
-                },
                 {
                     "@id": "bts:Stage"
                 },
@@ -2837,9 +2831,6 @@
                 {
                     "@id": "bts:MsTarget"
                 },
-                {
-                    "@id": "bts:SpeciesName"
-                },
                 {
                     "@id": "bts:Stage"
                 },
@@ -3000,9 +2991,6 @@
                 {
                     "@id": "bts:DirectionalBSseqLibrary"
                 },
-                {
-                    "@id": "bts:SpeciesName"
-                },
                 {
                     "@id": "bts:ReadStrandOrigin"
                 },
@@ -9688,44 +9676,8 @@
             "schema:isPartOf": {
                 "@id": "http://schema.biothings.io"
             },
-            "schema:rangeIncludes": [
-                {
-                    "@id": "bts:Multi-species"
-                },
-                {
-                    "@id": "bts:Notapplicable"
-                },
-                {
-                    "@id": "bts:Notcollected"
-                },
-                {
-                    "@id": "bts:Notspecified"
-                },
-                {
-                    "@id": "bts:Unknown"
-                }
-            ],
             "sms:displayName": "speciesName",
             "sms:required": "sms:true",
-            "sms:validationRules": [
-                "allowOther"
-            ]
-        },
-        {
-            "@id": "bts:Multi-species",
-            "@type": "rdfs:Class",
-            "rdfs:comment": "TBD",
-            "rdfs:label": "Multi-species",
-            "rdfs:subClassOf": [
-                {
-                    "@id": "bts:SpeciesName"
-                }
-            ],
-            "schema:isPartOf": {
-                "@id": "http://schema.biothings.io"
-            },
-            "sms:displayName": "Multi-species",
-            "sms:required": "sms:false",
             "sms:validationRules": []
         },
         {