Is ontology URL not supported for characteristics[organism]? #190
Description
Hi, I am testing validating of SDRF-proteomics file and in the official documentation for SDRF (https://github.com/bigbio/proteomics-sample-metadata/tree/master/sdrf-proteomics) it was mentioned that
Ontology url (Computer readable): Users can provide the corresponding URI (Uniform Resource Identifier) of the ontology/CV term as a value. This is recommended for enriched files where the user does not want to use intermediate tools to map from free text to ontology/CV terms.
source name characteristics[organism] Sample 1 http://purl.obolibrary.org/obo/NCBITaxon_9606 Sample 2 http://purl.obolibrary.org/obo/NCBITaxon_9606
When testing using the following SDRF file
source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[cell type] characteristics[biological replicate] characteristics[biological replicate] characteristics[age] characteristics[developmental stage] characteristics[sex] characteristics[ancestry category] characteristics[individual] material type assay name technology type comment[proteomics data acquisition method] comment[label] comment[instrument] comment[fraction identifier] comment[technical replicate] comment[cleavage agent details] comment[modification parameters] comment[modification parameters] comment[precursor mass tolerance] comment[fragment mass tolerance] comment[file uri] comment[data file] factor value[organism part] PXD004684-Sample-1 http://purl.obolibrary.org/obo/NCBITaxon_9606 lung tumor-adjacent tissues control not available 1 1 not available not available male white not available tissue run 1 proteomic profiling by mass spectrometry NT=Data-Independent Acquisition;AC=NCIT:C161786 NT=label free sample;AC=MS:1002038 NT=Q Exactive Plus;AC=MS:1002634 1 1 NT=Trypsin;AC=MS:1001251 NT=Oxidation;AC=UNIMOD:35;MT=Variable;TA=M NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Variable 10 ppm 0.05 Da ftp://ftp.pride.ebi.ac.uk/pride-archive/2017/02/PXD004684/N294-1.raw N294-1.raw lung tumor-adjacent tissues PXD004684-Sample-1 http://purl.obolibrary.org/obo/NCBITaxon_9606 lung tumor-adjacent tissues control not available 1 1 not available not available male white not available tissue run 2 proteomic profiling by mass spectrometry NT=Data-Independent Acquisition;AC=NCIT:C161786 NT=label free sample;AC=MS:1002038 NT=Q Exactive Plus;AC=MS:1002634 1 2 NT=Trypsin;AC=MS:1001251 NT=Oxidation;AC=UNIMOD:35;MT=Variable;TA=M NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Variable 10 ppm 0.05 Da ftp://ftp.pride.ebi.ac.uk/pride-archive/2017/02/PXD004684/N294-2.raw N294-2.raw lung tumor-adjacent tissues PXD004684-Sample-2 http://purl.obolibrary.org/obo/NCBITaxon_9606 lung tumor-adjacent tissues control not available 2 2 not available not available male white not available tissue run 3 proteomic profiling by mass spectrometry NT=Data-Independent Acquisition;AC=NCIT:C161786 NT=label free sample;AC=MS:1002038 NT=Q Exactive Plus;AC=MS:1002634 1 1 NT=Trypsin;AC=MS:1001251 NT=Oxidation;AC=UNIMOD:35;MT=Variable;TA=M NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Variable 10 ppm 0.05 Da ftp://ftp.pride.ebi.ac.uk/pride-archive/2017/02/PXD004684/N295-1.raw N295-1.raw lung tumor-adjacent tissues
It resulted in an error on validation
parse_sdrf validate-sdrf --sdrf_file "9923cc1c-6aab-4cf5-bd0f-438d24bb9f7e.tsv"
{row: 0, column: "characteristics[organism]"}: "http://purl.obolibrary.org/obo/ncbitaxon_9606" the term name or title can't be found in the ontology -- ncbitaxon
{row: 1, column: "characteristics[organism]"}: "http://purl.obolibrary.org/obo/ncbitaxon_9606" the term name or title can't be found in the ontology -- ncbitaxon
{row: 2, column: "characteristics[organism]"}: "http://purl.obolibrary.org/obo/ncbitaxon_9606" the term name or title can't be found in the ontology -- ncbitaxon
There were validation errors.After replace the ontology URL with the exact organism name Homo sapiens
parse_sdrf validate-sdrf --sdrf_file "9923cc1c-6aab-4cf5-bd0f-438d24bb9f7e.tsv"
Everything seems to be fine. Well done.