From a2a4b1a16cef38bb4ec9d222430fd396c70ba225 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 20 Apr 2020 16:46:28 -0400 Subject: Schema changes from @LLTommy --- bh20sequploader/bh20seq-shex.rdf | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) (limited to 'bh20sequploader/bh20seq-shex.rdf') diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 8d3f5fc..6e646c7 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -7,6 +7,7 @@ PREFIX sio: PREFIX efo: PREFIX evs: PREFIX edam: +PREFIX wikidata: :submissionShape { MainSchema:host @:hostShape ; @@ -18,8 +19,8 @@ PREFIX edam: :hostShape { efo:EFO_0000532 [ obo:NCBITaxon_~ ] ; - obo:PATO_0000047 [ obo:NCIT_C20197 obo:NCIT_C27993 obo:NCIT_C17998 ] ; - sio:SIO_000115 xsd:string ; + sio:SIO_000115 xsd:string ?; + obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 ] ?; obo:PATO_0000011 xsd:integer ?; obo:NCIT_C42574 [ obo:UO_~ ] ?; sio:SIO_001167 xsd:string ?; @@ -27,20 +28,20 @@ PREFIX edam: } :sampleShape { - obo:OBI_0001895 xsd:string ; - sio:SIO_000115 xsd:string ; - sio:SIO_001167 xsd:string ; - evs:C25164 xsd:string ?; - obo:GAZ_00000448 [obo:GAZ_~] ?; + evs:C25164 xsd:string?; + obo:GAZ_00000448 [wikidata:~] ; + obo:OBI_0001895 xsd:string ?; + sio:SIO_001167 xsd:string ?; + sio:SIO_000115 xsd:string ?; obo:OBI_0001472 xsd:string ?; - obo:OBI_0001479 xsd:string ?; + obo:OBI_0001479 IRI {0,2}; } :submitterShape { - sio:SIO_000116 xsd:string ; - obo:NCIT_C37984 xsd:string ; + obo:NCIT_C42781 xsd:string ; + obo:NCIT_C37984 xsd:string ?; obo:NCIT_C37900 xsd:string ?; - obo:NCIT_C42781 xsd:string ?; + sio:SIO_000116 xsd:string ?; obo:OBI_0600047 xsd:string ?; sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/?; sio:SIO_000172 xsd:string ?; @@ -48,7 +49,7 @@ PREFIX edam: } :technologyShape { - obo:OBI_0600047 xsd:string ; + obo:OBI_0600047 IRI {0,2} ; obo:FLU_0000848 xsd:integer ?; efo:EFO_0002699 xsd:string ?; } -- cgit v1.2.3 From 85b85b676d7ecc218d9f84357b2e7ea0133eed94 Mon Sep 17 00:00:00 2001 From: lltommy Date: Tue, 21 Apr 2020 16:49:47 +0200 Subject: Updated shex and manditory fields and stuff --- bh20sequploader/bh20seq-schema.yml | 10 +++++----- bh20sequploader/bh20seq-shex.rdf | 4 ++-- example/minimal_example.yaml | 6 +----- scripts/from_genbank_to_fasta_and_yaml.py | 19 +++++++++++++------ 4 files changed, 21 insertions(+), 18 deletions(-) (limited to 'bh20sequploader/bh20seq-shex.rdf') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 57f3b3d..75308ab 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -66,6 +66,11 @@ $graph: - name: sampleSchema type: record fields: + sample_id: + doc: Id of the sample as defined by the submitter + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 collection_date: doc: Date when the sample was taken type: string @@ -111,11 +116,6 @@ $graph: type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_001167 - sample_id: - doc: Id of the sample as defined by the submitter - type: string? - jsonldPredicate: - _id: http://semanticscience.org/resource/SIO_000115 source_database_accession: doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here type: string? diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 6e646c7..59ee71b 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -28,11 +28,11 @@ PREFIX wikidata: } :sampleShape { - evs:C25164 xsd:string?; + sio:SIO_000115 xsd:string; obo:GAZ_00000448 [wikidata:~] ; + evs:C25164 xsd:string; obo:OBI_0001895 xsd:string ?; sio:SIO_001167 xsd:string ?; - sio:SIO_000115 xsd:string ?; obo:OBI_0001472 xsd:string ?; obo:OBI_0001479 IRI {0,2}; } diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml index ed578e2..0e36a25 100644 --- a/example/minimal_example.yaml +++ b/example/minimal_example.yaml @@ -1,13 +1,10 @@ id: placeholder host: - host_id: XX1 host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 sample: sample_id: XX - collector_name: John Doe - collecting_institution: Doe university collection_date: 2020-01 collection_location: http://www.wikidata.org/entity/Q148 @@ -18,5 +15,4 @@ technology: sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0008632 submitter: - submitter_name: John Doe - originating_lab: John Doe's kitchen \ No newline at end of file + authors: John Doe \ No newline at end of file diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 0c410d7..7e7c089 100644 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -1,5 +1,5 @@ from Bio import Entrez -Entrez.email = 'insert_your_email@gmail.com' +Entrez.email = 'another_email@gmail.com' import xml.etree.ElementTree as ET import yaml @@ -31,6 +31,8 @@ for term in term_list: tmp_list = [x.split('.')[0] for x in tmp_list] print(term, len(tmp_list)) + tmp_list=tmp_list +# tmp_list = tmp_list[0:2] # restricting to small run id_set.update([x.split('.')[0] for x in tmp_list]) @@ -78,7 +80,7 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x term_to_uri_dict[term] = uri species_to_taxid_dict = { - 'Homo sapiens': 9606 + 'Homo sapiens': 'http://purl.obolibrary.org/obo/NCBITaxon_9606' } @@ -108,8 +110,8 @@ if not os.path.exists(dir_fasta_and_yaml_today): 'submitter': {} } - info_for_yaml_dict['sample']['sample_id'] = accession_version + info_for_yaml_dict['sample']['source_database_accession'] = accession_version info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')]) @@ -163,7 +165,7 @@ if not os.path.exists(dir_fasta_and_yaml_today): if GBQualifier_name_text == 'host': GBQualifier_value_text_list = GBQualifier_value_text.split('; ') - info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0] + #info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0] # Removed if GBQualifier_value_text_list[0] in species_to_taxid_dict: info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[GBQualifier_value_text_list[0]] @@ -206,8 +208,13 @@ if not os.path.exists(dir_fasta_and_yaml_today): elif GBQualifier_name_text == 'isolate': info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text elif GBQualifier_name_text == 'db_xref': - info_for_yaml_dict['virus']['virus_species'] = int(GBQualifier_value_text.split('taxon:')[1]) - + info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1] + + + #Remove technology key if empty! + if (info_for_yaml_dict['technology']=={}): + del info_for_yaml_dict['key'] + with open(os.path.join(dir_fasta_and_yaml_today, '{}.fasta'.format(accession_version)), 'w') as fw: fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper())) -- cgit v1.2.3 From 7e085b2958d9bd4f0a2b1912cf259a05b56366bc Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 21 Apr 2020 13:22:53 -0400 Subject: Tweak handling of "coverage" also fix typo Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- bh20sequploader/bh20seq-schema.yml | 4 ++-- bh20sequploader/bh20seq-shex.rdf | 2 +- scripts/dict_ontology_standardization/ncbi_speciesman_source.csv | 2 +- scripts/from_genbank_to_fasta_and_yaml.py | 9 ++++++--- 4 files changed, 10 insertions(+), 7 deletions(-) (limited to 'bh20sequploader/bh20seq-shex.rdf') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index ebca35b..75308ab 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -162,12 +162,12 @@ $graph: _id: http://www.ebi.ac.uk/efo/EFO_0002699 sequencing_coverage: doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x) - type: ["null", float, int] + type: float? jsonldPredicate: _id: http://purl.obolibrary.org/obo/FLU_0000848 sequencing_coverage2: doc: If a second sequence technology was used you can submit its coverage here - type: ["null", float, int] + type: float? jsonldPredicate: _id: http://purl.obolibrary.org/obo/FLU_0000848 additional_technology_information: diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 59ee71b..31e714f 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -50,7 +50,7 @@ PREFIX wikidata: :technologyShape { obo:OBI_0600047 IRI {0,2} ; - obo:FLU_0000848 xsd:integer ?; + obo:FLU_0000848 xsd:double ?; efo:EFO_0002699 xsd:string ?; } diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv index 2905588..909cf37 100644 --- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv +++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv @@ -1,4 +1,4 @@ -nasopharyngeal swab, http://purl.obolibrary.org/obo/NCIT_C155831 +nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831 nasopharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831 respiratory swab,http://purl.obolibrary.org/obo/NCIT_C155831 naso-pharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831 diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 1a12513..00c0012 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -130,9 +130,12 @@ if not os.path.exists(dir_fasta_and_yaml_today): if field_in_yaml == 'sequencing_coverage': # A regular expression would be better! - info_for_yaml_dict['technology'][field_in_yaml] = ';'.join( - [x.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>') for x in tech_info_to_parse.split(';')] - ) + try: + info_for_yaml_dict['technology'][field_in_yaml] = float( + tech_info_to_parse.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>')) + except ValueError: + print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse) + pass elif field_in_yaml == 'sample_sequencing_technology': new_seq_tec_list = [] for seq_tec in tech_info_to_parse.split(';'): -- cgit v1.2.3 From a12fe94f174da766be612fbb2712b4db2ba98296 Mon Sep 17 00:00:00 2001 From: lltommy Date: Wed, 22 Apr 2020 19:41:27 +0200 Subject: Small changes all around, trying to make the importer/metadata better --- bh20sequploader/bh20seq-schema.yml | 4 ++-- bh20sequploader/bh20seq-shex.rdf | 25 +++++++++++++++---------- example/metadata.yaml | 8 ++++---- scripts/foreach.sh | 2 +- scripts/from_genbank_to_fasta_and_yaml.py | 12 ++++++++---- 5 files changed, 30 insertions(+), 21 deletions(-) (limited to 'bh20sequploader/bh20seq-shex.rdf') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 1ceebe2..80013c3 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -25,7 +25,7 @@ $graph: jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 host_sex: - doc: Sex of the host as defined in NCIT, IRI expected (http://purl.obolibrary.org/obo/NCIT_C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female), http://purl.obolibrary.org/obo/NCIT_C45908 (Intersex), or http://purl.obolibrary.org/obo/NCIT_C17998 (Unknown)) + doc: Sex of the host as defined in PATO, expect male () or female () type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/PATO_0000047 @@ -144,7 +144,7 @@ $graph: fields: sample_sequencing_technology: doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) - type: string + type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0600047 _type: "@id" diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 31e714f..8d0055e 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -23,35 +23,40 @@ PREFIX wikidata: obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 ] ?; obo:PATO_0000011 xsd:integer ?; obo:NCIT_C42574 [ obo:UO_~ ] ?; - sio:SIO_001167 xsd:string ?; + obo:NCIT_C25688 xsd:string ? ; efo:EFO_0000727 xsd:string ?; + obo:VO_0000002 xsd:string ?; + sio:SIO_001167 xsd:string ?; } :sampleShape { sio:SIO_000115 xsd:string; - obo:GAZ_00000448 [wikidata:~] ; evs:C25164 xsd:string; + obo:GAZ_00000448 [wikidata:~] ; obo:OBI_0001895 xsd:string ?; - sio:SIO_001167 xsd:string ?; - obo:OBI_0001472 xsd:string ?; + obo:NCIT_C41206 xsd:string ?; obo:OBI_0001479 IRI {0,2}; + obo:OBI_0001472 xsd:string ?; + sio:SIO_001167 xsd:string ?; } :submitterShape { obo:NCIT_C42781 xsd:string ; - obo:NCIT_C37984 xsd:string ?; - obo:NCIT_C37900 xsd:string ?; sio:SIO_000116 xsd:string ?; - obo:OBI_0600047 xsd:string ?; - sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/?; sio:SIO_000172 xsd:string ?; + obo:NCIT_C37984 xsd:string ?; + obo:OBI_0600047 xsd:string ?; + obo:NCIT_C37900 xsd:string ?; efo:EFO_0001741 xsd:string ?; + obo:NCIT_C19026 xsd:string ?; + sio:SIO_000115 /https:\u002F\u002Forcid.org\u002F.{4}-.{4}-.{4}-.{4}/?; } :technologyShape { - obo:OBI_0600047 IRI {0,2} ; - obo:FLU_0000848 xsd:double ?; + obo:OBI_0600047 IRI {0,2} ?; efo:EFO_0002699 xsd:string ?; + obo:FLU_0000848 xsd:double {0,2}; + sio:SIO_001167 xsd:string ?; } :virusShape{ diff --git a/example/metadata.yaml b/example/metadata.yaml index 57d90b5..d1b10c1 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -6,7 +6,7 @@ host: host_sex: http://purl.obolibrary.org/obo/NCIT_C27993 host_age: 20 host_age_unit: http://purl.obolibrary.org/obo/UO_0000036 - host_health_status: A condition or state at a particular time (Disease ontology) + host_health_status: A condition or state at a particular time host_treatment: Process in which the act is intended to modify or alter host status (Compounds) host_vaccination: List of vaccines given to the host (RRIDs?) additional_host_information: Field for additional host information @@ -29,15 +29,15 @@ virus: technology: sample_sequencing_technology: http://www.ebi.ac.uk/efo/EFO_0009173 sample_sequencing_technology2: http://www.ebi.ac.uk/efo/EFO_0009173 - sequence_assembly_method: Protocol used for assembly (CWL, WDL, NF, BCO?) + sequence_assembly_method: Protocol used for assembly sequencing_coverage: 70 submitter: - submitter_name: John Doe (ORCID?) + submitter_name: John Doe submitter_address: John Doe's adress originating_lab: John Doe kitchen lab_address: John Doe's address provider_sample_id: HmX submitter_sample_id: xXx authors: John Doe et all - submitter_orcid: https://orcid.org/0000-0000-0000-0000 (if this is here, others can be optional?) + submitter_orcid: https://orcid.org/0000-0000-0000-0000 \ No newline at end of file diff --git a/scripts/foreach.sh b/scripts/foreach.sh index 35b07b8..ddc9387 100755 --- a/scripts/foreach.sh +++ b/scripts/foreach.sh @@ -2,7 +2,7 @@ rm -rf validated fasta_and_yaml_* mkdir -p validated ./from_genbank_to_fasta_and_yaml.py -fasta_files=$(find fasta_and_yaml_20200421/ -name "*.fasta") +fasta_files=$(find fasta_and_yaml/ -name "*.fasta") for f in $fasta_files ; do yaml=$(echo $f | rev | cut -c7- | rev).yaml echo $f diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 00c0012..096a6af 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -8,10 +8,11 @@ import json import os from datetime import date -today = date.today().strftime("%Y%m%d") +#today = date.today().strftime("%Y%m%d") -dir_metadata_today = 'metadata_from_nuccore_{}'.format(today) -dir_fasta_and_yaml_today = 'fasta_and_yaml_{}'.format(today) + +dir_metadata_today = 'metadata_from_nuccore' #_{}'.format(today) +dir_fasta_and_yaml_today = 'fasta_and_yaml' #'.format(today) dir_dict_ontology_standardization = 'dict_ontology_standardization/' @@ -177,7 +178,10 @@ if not os.path.exists(dir_fasta_and_yaml_today): if len(GBQualifier_value_text_list) > 1: if GBQualifier_value_text_list[1] in ['male', 'female']: - info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1] + if GBQualifier_value_text_list[1]=='male': + info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" + elif GBQualifier_value_text_list[1]=='female': + info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000383" else: info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1] -- cgit v1.2.3 From 2d3f8b9707bd13433ca82449ad82dbc406a28f95 Mon Sep 17 00:00:00 2001 From: lltommy Date: Wed, 22 Apr 2020 20:43:09 +0200 Subject: Including restrictions to the host status --- bh20sequploader/bh20seq-options.yml | 9 +++++++++ bh20sequploader/bh20seq-schema.yml | 2 +- bh20sequploader/bh20seq-shex.rdf | 2 +- 3 files changed, 11 insertions(+), 2 deletions(-) (limited to 'bh20sequploader/bh20seq-shex.rdf') diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml index da47e1a..68f6e79 100644 --- a/bh20sequploader/bh20seq-options.yml +++ b/bh20sequploader/bh20seq-options.yml @@ -14,6 +14,15 @@ host_sex: Male: http://purl.obolibrary.org/obo/PATO_0000384 Female: http://purl.obolibrary.org/obo/PATO_0000383 +host_health_status: + healthy: http://purl.obolibrary.org/obo/NCIT_C115935 + asymptomatic: http://purl.obolibrary.org/obo/NCIT_C3833 + sympotmatic: http://purl.obolibrary.org/obo/NCIT_C25269 + admitted to hospital: http://purl.obolibrary.org/obo/GENEPIO_0002020 + discharged from hospital: http://purl.obolibrary.org/obo/GENEPIO_0001849 + dead: http://purl.obolibrary.org/obo/NCIT_C28554 + alive: http://purl.obolibrary.org/obo/NCIT_C37987 + sample_sequencing_technology: Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173 Illumina NextSeq 550: http://www.ebi.ac.uk/efo/EFO_0008566 diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 80013c3..232ccc6 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -44,7 +44,7 @@ $graph: _type: "@id" noLinkCheck: true host_health_status: - doc: A condition or state at a particular time + doc: A condition or state at a particular time, must be one of the following (obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987) type: string? jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688 host_treatment: diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 8d0055e..bb15f91 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -23,7 +23,7 @@ PREFIX wikidata: obo:PATO_0000047 [ obo:PATO_0000384 obo:PATO_0000383 ] ?; obo:PATO_0000011 xsd:integer ?; obo:NCIT_C42574 [ obo:UO_~ ] ?; - obo:NCIT_C25688 xsd:string ? ; + obo:NCIT_C25688 [obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987 ] ? ; efo:EFO_0000727 xsd:string ?; obo:VO_0000002 xsd:string ?; sio:SIO_001167 xsd:string ?; -- cgit v1.2.3 From 7ef2c5c45d3d1b6e71a08fd0bdf19c42ef9e1014 Mon Sep 17 00:00:00 2001 From: lltommy Date: Wed, 22 Apr 2020 21:23:32 +0200 Subject: Fixing ShEx expression, one ? too much --- bh20sequploader/bh20seq-shex.rdf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'bh20sequploader/bh20seq-shex.rdf') diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index bb15f91..246fd57 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -53,7 +53,7 @@ PREFIX wikidata: } :technologyShape { - obo:OBI_0600047 IRI {0,2} ?; + obo:OBI_0600047 IRI {0,2} ; efo:EFO_0002699 xsd:string ?; obo:FLU_0000848 xsd:double {0,2}; sio:SIO_001167 xsd:string ?; -- cgit v1.2.3