Merge branch 'master' of github.com:arvados/bh20-seq-resource

3 files changed, 37 insertions, 9 deletions

diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 1a441f0..2aebe80 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -451,8 +451,9 @@ def getDetailsForSeq():
 @app.route('/api/getSEQCountbytech', methods=['GET'])
 def getSEQCountbytech():
     query="""SELECT ?tech ?tech_label (count(?fasta) as ?fastaCount) WHERE 
-    {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047>  ?tech] 
-    BIND (concat(?tech,"_label") as ?tech_label)}
+    {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047>  ?tech] .
+     OPTIONAL {?tech <http://www.w3.org/2000/01/rdf-schema#label> ?tech_tmp_label } .
+     BIND(IF(BOUND(?tech_tmp_label), ?tech_tmp_label,?tech) as ?tech_label)}
     GROUP BY ?tech ?tech_label ORDER BY DESC (?fastaCount)
     """
     payload = {'query': query, 'format': 'json'}
@@ -505,8 +506,9 @@ def getSEQbyLocation():
 @app.route('/api/getSEQCountbyLocation', methods=['GET'])
 def getSEQCountbyLocation():
     query="""SELECT ?geoLocation ?geoLocation_label (count(?fasta) as ?fastaCount)  WHERE
-    {?fasta ?x [<http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation]
-    BIND (concat(?geoLocation,"_label") as ?geoLocation_label)}
+    {?fasta ?x [<http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation] .
+    Optional {?geoLocation <http://www.w3.org/2000/01/rdf-schema#label> ?geoLocation_tmp_label}
+    BIND(IF(BOUND(?geoLocation_tmp_label), ?geoLocation_tmp_label, ?geoLocation) as ?geoLocation_label)}
     GROUP BY ?geoLocation ?geoLocation_label ORDER BY DESC (?fastaCount)
     """
     payload = {'query': query, 'format': 'json'}
@@ -521,9 +523,10 @@ def getSEQCountbyLocation():
 def getSEQCountbySpecimenSource():
     query="""SELECT ?specimen_source ?specimen_source_label (count(?fasta) as ?fastaCount)  WHERE
     {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479>  ?specimen_source]
-    BIND (concat(?specimen_source,"_label") as ?specimen_source_label)}
-    GROUP BY ?specimen_source ?specimen_source_label
-    ORDER BY DESC (?fastaCount)
+     Optional { ?specimen_source <http://www.w3.org/2000/01/rdf-schema#label> ?specimen_source_tmp_label}
+     BIND(IF(BOUND(?specimen_source_tmp_label), ?specimen_source_tmp_label ,?specimen_source) as ?specimen_source_label)}
+     GROUP BY ?specimen_source ?specimen_source_label
+     ORDER BY DESC (?fastaCount)
     """
     payload = {'query': query, 'format': 'json'}
     r = requests.get(baseURL, params=payload)
diff --git a/paper/paper.md b/paper/paper.md
index 6a5d624..4df267f 100644
--- a/paper/paper.md
+++ b/paper/paper.md
@@ -15,7 +15,7 @@ authors:
     orcid: 0000
     affiliation: 3
   - name: Thomas Liener
-    orcid: 0000
+    orcid: https://orcid.org/0000-0003-3257-9937
     affiliation: 4
   - name: Erik Garrison
     orcid: 0000
@@ -52,7 +52,9 @@ affiliations:
     index: 1
   - name: Curii, Boston, USA
     index: 2
-  - name: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA.
+  - name: Thomas Liener Consultancy
+    index: 4
+  - name: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064, USA
     index: 5
   - name: Department of Computer Science, Faculty of Sciences, Vrije Universiteit Amsterdam, The Netherlands
     index: 6
diff --git a/semantic_enrichment/labels.ttl b/semantic_enrichment/labels.ttl
index b4e5d1f..cd0464a 100644
--- a/semantic_enrichment/labels.ttl
+++ b/semantic_enrichment/labels.ttl
@@ -13,6 +13,13 @@
 <http://purl.obolibrary.org/obo/OBI_0001895> <http://www.w3.org/2000/01/rdf-schema#label> "specimen collector" .
 <http://edamontology.org/data_2091> <http://www.w3.org/2000/01/rdf-schema#label> "Accession" .
 <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> <http://www.w3.org/2000/01/rdf-schema#label> "collection date" .
+<http://purl.obolibrary.org/obo/PATO_0000047> <http://www.w3.org/2000/01/rdf-schema#label> "biological sex" .
+<http://purl.obolibrary.org/obo/PATO_0000011> <http://www.w3.org/2000/01/rdf-schema#label> "age" .
+<http://purl.obolibrary.org/obo/NCIT_C42574> <http://www.w3.org/2000/01/rdf-schema#label> "Unit of Time".
+<http://purl.obolibrary.org/obo/NCIT_C25688> <http://www.w3.org/2000/01/rdf-schema#label> "Status" .
+<http://www.ebi.ac.uk/efo/EFO_0000727> <http://www.w3.org/2000/01/rdf-schema#label> "treatment" .
+<http://purl.obolibrary.org/obo/VO_0000002> <http://www.w3.org/2000/01/rdf-schema#label> "vaccination" .
+<http://semanticscience.org/resource/SIO_001014> <http://www.w3.org/2000/01/rdf-schema#label> "ethnicity" .
 <http://purl.obolibrary.org/obo/NCIT_C3833> <http://www.w3.org/2000/01/rdf-schema#label> "Asymptomatic" .
 <http://purl.obolibrary.org/obo/NCIT_C25269> <http://www.w3.org/2000/01/rdf-schema#label> "Symptomatic" .
 <http://purl.obolibrary.org/obo/GENEPIO_0002020> <http://www.w3.org/2000/01/rdf-schema#label> "admitted to hospital" .
@@ -22,3 +29,19 @@
 <http://purl.obolibrary.org/obo/NCIT_C115935> <http://www.w3.org/2000/01/rdf-schema#label> "Healthy" .
 <http://purl.obolibrary.org/obo/PATO_0000384> <http://www.w3.org/2000/01/rdf-schema#label> "male".
 <http://purl.obolibrary.org/obo/PATO_0000383> <http://www.w3.org/2000/01/rdf-schema#label> "female" .
+<http://www.ebi.ac.uk/efo/EFO_0009173> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina NextSeq 500" .
+<http://www.ebi.ac.uk/efo/EFO_0008632> <http://www.w3.org/2000/01/rdf-schema#label> "ONT MinION" .
+<http://purl.obolibrary.org/obo/NCIT_C146818> <http://www.w3.org/2000/01/rdf-schema#label> " Oxford Nanopore Sequencing" .
+<http://www.ebi.ac.uk/efo/EFO_0004205> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina MiSeq" .
+<http://purl.obolibrary.org/obo/OBI_0000759> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina" .
+<http://purl.obolibrary.org/obo/NCIT_C125894> <http://www.w3.org/2000/01/rdf-schema#label> "Ion Semiconductor Sequencing".
+<http://purl.obolibrary.org/obo/NCIT_C19641> <http://www.w3.org/2000/01/rdf-schema#label> "Dideoxy Chain Termination DNA Sequencing" .
+<http://purl.obolibrary.org/obo/NCIT_C155831> <http://www.w3.org/2000/01/rdf-schema#label> "Nasopharyngeal Swab Specimen" .
+<http://purl.obolibrary.org/obo/NCIT_C155835> <http://www.w3.org/2000/01/rdf-schema#label> "Oropharyngeal Swab Specimen" .
+<http://purl.obolibrary.org/obo/NCIT_C13195> <http://www.w3.org/2000/01/rdf-schema#label> "Bronchoalveolar Lavage Fluid" .
+<http://purl.obolibrary.org/obo/NCIT_C13278> <http://www.w3.org/2000/01/rdf-schema#label> "Sputum" .
+<http://purl.obolibrary.org/obo/NCIT_C13347> <http://www.w3.org/2000/01/rdf-schema#label> "Aspirate" .
+<http://purl.obolibrary.org/obo/NCIT_C13234> <http://www.w3.org/2000/01/rdf-schema#label> "Feces" .
+<http://purl.obolibrary.org/obo/NCIT_C13325> <http://www.w3.org/2000/01/rdf-schema#label> "Serum" .
+<http://purl.obolibrary.org/obo/NCIT_C13275> <http://www.w3.org/2000/01/rdf-schema#label> "Saliva" .
+<http://purl.obolibrary.org/obo/NCIT_C132119> <http://www.w3.org/2000/01/rdf-schema#label> "Nasal Swab" .
\ No newline at end of file