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The ISAvalidator, ISA converter and BII data manager tools
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ISAvalidator: issue with multiple terms of controlled vocab #62

Open althonos opened 7 years ago

althonos commented 7 years ago

Hi there, when I tried to add controlled vocabularies to the parameters of protocols in my Investigation file, the validator gave me the following error: Problem while mapping the class 'Protocol': 3 though I think I did it the right way, so it might be an issue with the validator...

Here's my i_Investigation.txt: i_Investigation.txt

and the relevant section:

STUDY PROTOCOLS
Study Protocol Name "Sample collection" "Extraction"    "Chromatography"    "Mass spectrometry" "Data transformation"   "Metabolite identification"
Study Protocol Type "Sample collection" "Extraction"    "Chromatography"    "Mass spectrometry" "Data transformation"   "Metabolite identification"
Study Protocol Type Term Accession Number   "http://purl.bioontology.org/ontology/CRISP/4009-0034"  "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C61575" "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16431" "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17156" "http://purl.obolibrary.org/obo/OBI_0200000"    "http://purl.obolibrary.org/obo/MI_2131"
Study Protocol Type Term Source REF "CRISP" "NCIT"  "NCIT"  "NCIT"  "OBI"   "MI"
Study Protocol Description  ""  ""  ""  ""  ""  ""
Study Protocol URI  ""  ""  ""  ""  ""  ""
Study Protocol Version  ""  ""  ""  ""  ""  ""
Study Protocol Parameters Name  ""  "Post Extraction;Derivatization"    "Chromatography Instrument;Column type;Column model"    "Instrument software;Detector mode;Spectrum representation;Inlet type;Number of scans;Scan m/z range;Detector;Instrument serial number;Raw data file checksum type;Mass analyzer;Instrument manufacturer;Raw data file format;Scan polarity;Raw data file checksum value;Instrument software version;Native spectrum identifier format;Instrument;Data file content;Time range;Ion source"  ""  "Data Transformation software;Data Transformation software version"
Study Protocol Parameters Name Term Accession Number    ""  ";http://purl.obolibrary.org/obo/CHMO_0001485"  ";;"    "http://purl.obolibrary.org/obo/MS_1000531;http://purl.obolibrary.org/obo/MS_1000027;http://purl.obolibrary.org/obo/MS_1000525;;;;;;;;;;;;;;;;;"    ""  "http://purl.obolibrary.org/obo/MS_1000531;"
Study Protocol Parameters Name Term Source REF  ""  ";CHMO" ";;"    "MS;MS;MS;;;;;;;;;;;;;;;;;" ""  "MS;"
Study Protocol Components Name  ""  ""  ""  ""  ""  ""
Study Protocol Components Type  ""  ""  ""  ""  ""  ""
Study Protocol Components Type Term Accession Number    ""  ""  ""  ""  ""  ""
Study Protocol Components Type Term Source REF  ""  ""  ""  ""  ""  ""
agbeltran commented 7 years ago

Hi @althonos Could you provide all the ISA-Tab files for us to test? Also, if you are after validating them, you may also have a look at the python-based ISA-API, which includes a new validator. Thanks.

althonos commented 7 years ago

Hi @agbeltran , I'll give a try to python isatools. thanks !

The following contains all my ISA-Tab files ( MTBLS267.zip ) and after a test, it looks like removing the controlled values references makes the validation successful again.