1) unify data types, 2) bugs fixed, 3) allow values and/or units for …

…material, animal age and collection countries

docs/image_data_type.md

@@ -2,21 +2,22 @@
 
 [BioSamples](http://www.ebi.ac.uk/biosamples) takes sample records with a set of attributes. Each attribute has a name and a value. It can also have 'Units', or a 'Term Source' and a 'Term Source ID'. The Term Source and ID allow us to refer to entries in other databases or ontologies. This is fully described on the [BioSamples help pages](http://www.ebi.ac.uk/biosamples/help/st_scd.html). The following section describes the expectations for each data type within IMAGE.
 
-### date
+### number
 
-Dates should be reported in an [ISO 8601](https://en.wikipedia.org/wiki/ISO_8601) format,  YYYY-MM-DD for dates or YYYY-MM for months. To ensure clarity, the format must be reported as the 'units'.
+A number, with units specified. BioSamples recommends that units are given without abbreviations. Terms defined in the [UO](http://www.ebi.ac.uk/ols/ontologies/uo) are encouraged to be used. For example, a birth weight could have a value of 1.3 and the units specified as '[kilogram](http://www.ebi.ac.uk/ols/ontologies/uo/terms?short_form=UO_0000009)' .
 
-### NCBI taxon ID
+### text
 
-A species name and identifier from the [NCBI Taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy). For example, [human](http://www.ncbi.nlm.nih.gov/taxonomy/9606) would be described in the term with value of 'Homo sapiens', term source as 'NCBI Taxonomy' and term source ID as 9606.
+Text, using US English spellings. No check on this type.
 
-### number
+### limited value
 
-A number, with units specified. BioSamples recommends that units are given without abbreviations. Terms defined in the [UO](http://www.ebi.ac.uk/ols/ontologies/uo) are encouraged to be used. For example, a birth weight could have a value of 1.3 and the units specified as '[kilogram](http://www.ebi.ac.uk/ols/ontologies/uo/terms?short_form=UO_0000009)' .
+Text type, but the allowed values are limited which either defined in the allowed values or point to other samples. Samples can be referred to in two ways. If the sample you need to reference is in the submission, use the sample name. If 
+the sample was already submitted, use the BioSample ID (e.g. SAMEA2821491).
 
-### text
+### date
 
-Text, using US English spellings.
+Dates should be reported in an [ISO 8601](https://en.wikipedia.org/wiki/ISO_8601) format,  YYYY-MM-DD for dates or YYYY-MM for months. To ensure clarity, the format must be reported as the 'units'.
 
 ### URI
 
@@ -30,10 +31,8 @@ A URI,  such as 'http://www.imageh2020.eu/'. Depending on the context, http, ftp
 
 Digital Object Identifier (DOI) can unambiguously point to one publication, which can be resolved [here](http://www.doi.org/).
 
-### ontology term
+### ontology id
 
 A reference to an ontology term. The attribute value should be the term label. The term source should be the ontology used, and the term source ID should be an ID from that ontology. For example, cerebral cortex could be  described with an ontology term from 'UBERON' with ontology ID of 'UBERON:0000956' and the attribute value is 'cerebral cortex'. Though in the experiment submission, direct links to ontologies cannot be submitted as attributes. The use of ontology terms is still encouraged by setting the attribute value to exactly match the term name in the ontology. 
+A special case is taxonomy. A species name and identifier from the [NCBI Taxonomy database](http://www.ncbi.nlm.nih.gov/taxonomy). For example, [human](http://www.ncbi.nlm.nih.gov/taxonomy/9606) would be described in the term with value of 'Homo sapiens', term source as 'NCBI Taxonomy' and term source ID as 9606.
 
-### sample
-
-Samples can be referred to in two ways. If the sample you need to reference is in the submission, use the sample name. If the sample was already submitted, use the BioSample ID (e.g. SAMEA2821491).

docs/image_sample_metadata.md

@@ -28,19 +28,19 @@ Mandatory:
 
   * `Submission title` (*text*) A descriptive title for the submission
   * `Material` (*ontology_id*) type of the sample, either animal(organism) or sample (specimen from organism) Allowed values are:
-    * [Organism](http://purl.obolibrary.org/obo/OBI_0100026)
-    * [Specimen from organism](http://purl.obolibrary.org/obo/OBI_0001479)
+    * [organism](http://purl.obolibrary.org/obo/OBI_0100026)
+    * [specimen from organism](http://purl.obolibrary.org/obo/OBI_0001479)
 
   * `Person last name` (*text*) the last name of the submitter or contact for these samples, multiple persons can be provided
-  * `Person email` (*uri_value*) email of contact person
+  * `Person email` (*uri*) email of contact person
   * `Person affiliation` (*text*) affiliation of person
   * `Person role` (*text*) the role (type of the contribution) made by the person
   * `Organization name` (*text*) Organization name, multiple can be supplied, but at least one must be the name of the gene bank
   * `Organization role` (*ontology_id*) the role of the organization, e.g. biobank, funder
   * `Gene bank name` (*text*) The name of the gene bank that the data of this submission belongs to, ideally use the value stored in EUGENA
   * `Gene bank country` (*limited value*) Country in which the gene bank resides, particularly important when different countries use the same database infrastructure, e.g. CryoWeb. The controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary
   * `Data source type` (*limited value*) the type of the data source the current Inject tool can handle Allowed values are:
-    * CyroWeb
+    * CryoWeb
     * CRB-Anim
     * Template
 
@@ -52,15 +52,30 @@ Recommended:
   * `Submission description` (*text*) A brief description of the submission
   * `Person first name` (*text*) the first name of the submitter or contact for these samples, multiple persons can be provided
   * `Organization address` (*text*) The address of the organisation, multiple can be supplied
-  * `Organization country` (*text*) Country in which organization resides, the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary Allowed values are:
-    * the controlled vocabulary for countries is from INSDC http://www.insdc.org/documents/country-qualifier-vocabulary
+  * `Organization country` (*text*) Country in which organization resides, the organization list is maintained at https://github.com/cnr-ibba/IMAGE-InjectTool/blob/devel/django-data/image/image_app/management/commands/organization_list.csv Allowed values are:
+    * [France](http://purl.obolibrary.org/obo/NCIT_C16592)
+    * [Egypt](http://purl.obolibrary.org/obo/NCIT_C16530)
+    * [Colombia](http://purl.obolibrary.org/obo/NCIT_C16449)
+    * [Switzerland](http://purl.obolibrary.org/obo/NCIT_C17181)
+    * [Netherlands](http://purl.obolibrary.org/obo/NCIT_C16903)
+    * [Germany](http://purl.obolibrary.org/obo/NCIT_C16636)
+    * [Italy](http://purl.obolibrary.org/obo/NCIT_C16761)
+    * [Hungary](http://purl.obolibrary.org/obo/NCIT_C16699)
+    * [Morocco](http://purl.obolibrary.org/obo/NCIT_C16878)
+    * [Spain](http://purl.obolibrary.org/obo/NCIT_C17152)
+    * [Argentina](http://purl.obolibrary.org/obo/NCIT_C16305)
+    * [Sweden](http://purl.obolibrary.org/obo/NCIT_C17180)
+    * [United Kingdom](http://purl.obolibrary.org/obo/NCIT_C17233)
+    * [Poland](http://purl.obolibrary.org/obo/NCIT_C17002)
+    * [Portugal](http://purl.obolibrary.org/obo/NCIT_C17006)
+    * [Austria](http://purl.obolibrary.org/obo/NCIT_C16312)
 
 
 Optional:
 
   * `Description` (*text*) A brief description of the sample
   * `Person initial` (*text*) the initial of the submitter or contact for these samples, multiple persons can be provided
-  * `Organization uri` (*uri_value*) the websites of orgnization, multiple can be supplied
+  * `Organization uri` (*uri*) the websites of orgnization, multiple can be supplied
   * `Publication DOI` (*doi*) Publication associated with sample, supplied as the digital object identifier which can unambiguously point to the publication
 
 ### Animal
@@ -89,7 +104,7 @@ Recommended:
 
 Optional:
 
-  * `Child of` (*BioSample ID or Alternative animal ID*) Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted
+  * `Child of` (*text*) Father and/or Mother's animal ID whose record must also be present as part of the subission or BioSamples ID if sample has been previously submitted
 
 ### Sample
 
@@ -116,7 +131,7 @@ Recommended:
   * `Collection place longitude` (*number*) longitude of the place where the sample was collected
   * `Developmental stage` (*ontology_id*) developmental stage of the animal from which the specimen is collected
   * `Physiological stage` (*ontology_id*) physiological stage of the animal from which the specimen is collected
-  * `Availability` (*uri_value or text*) Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:[email protected]'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts. Allowed values are:
+  * `Availability` (*text*) Either an e-mail address to contact about availability or a link to a web page giving information on who to contact. E-mail addresses should be prefixed with 'mailto:', e.g. 'mailto:[email protected]'. In either case, long term support of the web page or e-mail address is necessary. Group e-mail addresses are preferable to indiviudal accounts. Allowed values are:
     * no longer available
     * mailto:a.valid@email