Merge branch 'master' into develop

isatools/create/i_investigation.txt

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+ONTOLOGY SOURCE REFERENCE
+Term Source Name	OBI	STATO	STATO
+Term Source File			
+Term Source Version			
+Term Source Description	Ontology for Biomedical Investigations	Ontology for Statistical Methods	Ontology for Statistical Methods
+INVESTIGATION
+Investigation Identifier	
+Investigation Title	
+Investigation Description	
+Investigation Submission Date	
+Investigation Public Release Date	
+INVESTIGATION PUBLICATIONS
+Investigation PubMed ID
+Investigation Publication DOI
+Investigation Publication Author List
+Investigation Publication Title
+Investigation Publication Status
+Investigation Publication Status Term Accession Number
+Investigation Publication Status Term Source REF
+INVESTIGATION CONTACTS
+Investigation Person Last Name
+Investigation Person First Name
+Investigation Person Mid Initials
+Investigation Person Email
+Investigation Person Phone
+Investigation Person Fax
+Investigation Person Address
+Investigation Person Affiliation
+Investigation Person Roles
+Investigation Person Roles Term Accession Number
+Investigation Person Roles Term Source REF
+STUDY
+Study Identifier	b5e5a99f-1911-4e6e-909a-653d10aa072b
+Study Title	boilerplate title
+Study Description	boilerplate study description (testing purpose)
+Study Submission Date	2017-06-07
+Study Public Release Date	2017-07-07
+Study File Name	s_study.txt
+Comment[number of study groups]	8.0
+Comment[study group size]	3.0
+STUDY DESIGN DESCRIPTORS
+Study Design Type	intervention design	full factorial design	balanced design
+Study Design Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000115	http://purl.obolibrary.org/obo/STATO_0000270	http://purl.obolibrary.org/obo/STATO_0000003
+Study Design Type Term Source REF	OBI	STATO	STATO
+STUDY PUBLICATIONS
+Study PubMed ID	12345678
+Study Publication DOI	
+Study Publication Author List	A. Robertson, B. Robertson
+Study Publication Title	boiler plate publication
+Study Publication Status	published
+Study Publication Status Term Accession Number	
+Study Publication Status Term Source REF	
+STUDY FACTORS
+Study Factor Name	agent	dose	duration of exposure
+Study Factor Type	perturbation agent	intensity	time
+Study Factor Type Term Accession Number			
+Study Factor Type Term Source REF			
+STUDY ASSAYS
+Study Assay File Name	a_mp_FIA_positive_ms.txt	a_mp_FIA_negative_ms.txt	a_mp_LC_positive_ms.txt	a_mp_LC_negative_ms.txt	a_tp_ngs.txt
+Study Assay Measurement Type	metabolite profiling	metabolite profiling	metabolite profiling	metabolite profiling	transcription profiling
+Study Assay Measurement Type Term Accession Number					
+Study Assay Measurement Type Term Source REF					
+Study Assay Technology Type	FIA-positive mass spectrometry	FIA-negative mass spectrometry	LC-positive mass spectrometry	LC-negative mass spectrometry	nucleic acid sequencing
+Study Assay Technology Type Term Accession Number					
+Study Assay Technology Type Term Source REF					
+Study Assay Technology Platform					
+STUDY PROTOCOLS
+Study Protocol Name	sample collection	metabolite extraction	FIA-positive mass spectrometry	metabolite extraction	FIA-negative mass spectrometry	metabolite extraction	LC-positive mass spectrometry	metabolite extraction	LC-negative mass spectrometry	RNA extraction	nucleic acid library preparation	nucleic acid sequencing
+Study Protocol Type	sample collection	material separation	mass spectrometry	material separation	mass spectrometry	material separation	mass spectrometry	material separation	mass spectrometry	material separation	material labeling	data collection
+Study Protocol Type Term Accession Number												
+Study Protocol Type Term Source REF												
+Study Protocol Description												
+Study Protocol URI												
+Study Protocol Version												
+Study Protocol Parameters Name			randomized run order;injection mode;mass spectrometry instrument;scan polarity		randomized run order;injection mode;mass spectrometry instrument;scan polarity		randomized run order;injection mode;mass spectrometry instrument;scan polarity		randomized run order;injection mode;mass spectrometry instrument;scan polarity			
+Study Protocol Parameters Name Term Accession Number			;;;		;;;		;;;		;;;			
+Study Protocol Parameters Name Term Source REF			;;;		;;;		;;;		;;;			
+Study Protocol Components Name												
+Study Protocol Components Type												
+Study Protocol Components Type Term Accession Number												
+Study Protocol Components Type Term Source REF												
+STUDY CONTACTS
+Study Person Last Name	Plate
+Study Person First Name	Boiler
+Study Person Mid Initials	
+Study Person Email	
+Study Person Phone	
+Study Person Fax	
+Study Person Address	
+Study Person Affiliation	boiler plate affiliation
+Study Person Roles	
+Study Person Roles Term Accession Number	
+Study Person Roles Term Source REF	

isatools/create/isa-possible-workflows.json

@@ -0,0 +1,146 @@
+{
+  "assay_type": {
+    "name": "mass spectrometry",
+    "abbreviation": "MS",
+    "uri": "",
+    "sample_injection_type": {
+      "name": "direct infusion assay",
+      "abbreviation": "DIA",
+      "polarity_mode": [
+        "positive_mode",
+        "negative mode"
+      ],
+      "number_of_injection": ""
+    },
+    "sample_injection_type": {
+      "name": "liquid chromatography assay",
+      "abbreviation": "LC",
+      "polarity_mode": [
+        "positive_mode",
+        "negative mode"
+      ],
+      "number_of_injection": ""
+    },
+    "sample_injection_type": {
+      "name": "gas chromatography assay",
+      "abbreviation": "GC",
+      "polarity_mode": [
+        "positive_mode",
+        "negative mode"
+      ],
+      "number_of_injection": ""
+    }
+  },
+  "assay_type": {
+  "name": "nmr spectroscopy",
+  "abbreviation": "NMR",
+  "uri": "",
+  "sample_injection_type": {
+    "name": "liquid chromatography assay",
+    "abbreviation": "LC",
+    "acquisition": {
+      "dimension": {
+        "name": "1 dimension NMR",
+        "abbreviation": "1D",
+        "nuclei": [
+          "1H",
+          "13C"
+        ],
+        "pulse_sequence": [
+          "CPMG",
+          "NOESY",
+          "J-RES"
+        ]
+      }
+    },
+    "number_of_injection": ""
+  },
+  "sample_injection_type": {
+    "name": "liquid chromatography assay",
+    "abbreviation": "LC",
+    "acquisition": {
+      "dimension": {
+        "name": "2 dimension NMR",
+        "abbreviation": "2D",
+        "nuclei": [
+          "1H-1H",
+          "1H-13C",
+          "13C-13C"
+        ],
+        "pulse_sequence": [
+          "HSQC",
+          "TOCSY",
+          "TOESY",
+          "other"
+        ]
+      }
+    },
+    "number_of_injection": ""
+  },
+  "sample_injection_type": {
+    "name": "gas chromatography assay",
+    "abbreviation": "GC",
+    "acquisition": {
+      "dimension": {
+        "name": "1 dimension NMR",
+        "abbreviation": "1D",
+        "nuclei": [
+          "1H",
+          "13C"
+        ],
+        "pulse_sequence": [
+          "CPMG",
+          "NOESY",
+          "J-RES"
+        ]
+      }
+    },
+    "number_of_injection": ""
+  },
+  "sample_injection_type": {
+    "name": "gas chromatography assay",
+    "abbreviation": "GC",
+    "acquisition": {
+      "dimension": {
+        "name": "2 dimension NMR",
+        "abbreviation": "2D",
+        "nuclei": [
+          "1H-1H",
+          "1H-13C",
+          "13C-13C"
+        ],
+        "pulse_sequence": [
+          "HSQC",
+          "TOCSY",
+          "TOESY",
+          "other"
+        ]
+      }
+    },
+    "number_of_injection": ""
+  }
+},
+  "assay_type": {
+    "name" : "dna microarray",
+    "abbreviation" : "genechip",
+    "uri" : "",
+    "array_designs" : {
+      "name" : "",
+      "uri" : ""
+    },
+    "acquisition" : {
+      "channels" : ["1","2","3"]
+    },
+    "number_of_techrep": ""
+  },
+  "assay_type" : {
+    "name" : "dna sequencing",
+    "abbreviation" : "NGS",
+    "uri" : "",
+    "number_of_libraries":"",
+    "acquisition" :{
+      "multiplex_identifier":["",""]
+    },
+    "number_of_techrep": ""
+  }
+}