add missing links

cimendes · cimendes · commit f2e5c4f5bd2e · 2020-07-09T19:32:30.000+01:00
diff --git a/README.md b/README.md
@@ -30,39 +30,45 @@ supporting materials are freely available in this repository.
 **Table 1:** Resources that form the PHA4GE SARS-CoV-2 contextual data specification package available  in this repository.
 | File Name 	| Resource 	| Description 	|  	|
 |-	|-	|-	|-	|
-| [PHA4GE SARS-CoV-2 Contextual Data Template.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template%202.1.xlsx) 	| Collection template and controlled vocabulary pick lists 	| Spreadsheet-based collection form containing different fields (identifiers and accessions, sample collection and processing, sequencing, host information, host exposure information, bioinformatics and QC metrics, author acknowledgements). Fields are colour-coded to indicate required, recommended or optional status. Many fields offer pick lists of controlled vocabulary. Vocabulary lists are also available in a separate tab. 	|  	|
-| [PHA4GE SARS-CoV-2 Contextual Data Template.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template%202.1.xlsx)	| Reference guide 	| Field definitions, guidance, and examples are provided as a separate tab in the collection template .xlsx file. 	|  	|
-| [PHA4GE Contextual Data SOP.docx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20Contextual%20Data%20SOP%201.0.docx)	| Collection template SOP 	| Step-by-step instructions for using the collection template are provided in the SOP. Ethical, practical, and privacy considerations are also discussed. Examples and instructions for structuring sample descriptions as well as sourcing additional standardized terms (outside those provided in pick lists) are also discussed. 	|  	|
-| [PHA4GE SARS-CoV-2 Contextual Data Template.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template%202.1.xlsx) 	| PHA4GE fields to metadata standards mapping 	| PHA4GE fields are mapped to existing metadata standards such as the [Sample Application Standard](https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards), [MIxS 5.0](https://gensc.org/mixs/), and the [MIGS Virus Host-associated attribute package](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIGS.eu.host-associated.5.0/). Mappings are available in the Reference guide tab. Mappings highlight which fields of these standards are considered useful for SARS-CoV-2 public health surveillance and investigations, and which fields are considered not applicable. 	|  	|
-| [PHA4GE to Sequence Repository Field Mappings.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20to%20Sequence%20Repository%20Field%20Mappings%201.0.xlsx) 	| ENA, NCBI and GISAID submission requirements to PHA4GE field mappings 	| Many PHA4GE fields have been sourced from public repository submission requirements. The different repositories have different requirements and field names. Repository submission fields have been mapped to PHA4GE fields to demonstrate equivalencies and divergences. 	|  	|
+| [PHA4GE SARS-CoV-2 Contextual Data Template.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template.xlsx) 	| Collection template and controlled vocabulary pick lists 	| Spreadsheet-based collection form containing different fields (identifiers and accessions, sample collection and processing, sequencing, host information, host exposure information, bioinformatics and QC metrics, author acknowledgements). Fields are colour-coded to indicate required, recommended or optional status. Many fields offer pick lists of controlled vocabulary. Vocabulary lists are also available in a separate tab. 	|  	|
+| [PHA4GE SARS-CoV-2 Contextual Data Template.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template.xlsx)	| Reference guide 	| Field definitions, guidance, and examples are provided as a separate tab in the collection template .xlsx file. 	|  	|
+| [PHA4GE Contextual Data SOP.docx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20Contextual%20Data%20SOP.docx)	| Collection template SOP 	| Step-by-step instructions for using the collection template are provided in the SOP. Ethical, practical, and privacy considerations are also discussed. Examples and instructions for structuring sample descriptions as well as sourcing additional standardized terms (outside those provided in pick lists) are also discussed. 	|  	|
+| [PHA4GE SARS-CoV-2 Contextual Data Template.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template.xlsx) 	| PHA4GE fields to metadata standards mapping 	| PHA4GE fields are mapped to existing metadata standards such as the [Sample Application Standard](https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards), [MIxS 5.0](https://gensc.org/mixs/), and the [MIGS Virus Host-associated attribute package](https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIGS.eu.host-associated.5.0/). Mappings are available in the Reference guide tab. Mappings highlight which fields of these standards are considered useful for SARS-CoV-2 public health surveillance and investigations, and which fields are considered not applicable. 	|  	|
+| [PHA4GE to Sequence Repository Field Mappings.xlsx](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20to%20Sequence%20Repository%20Field%20Mappings.xlsx) 	| ENA, NCBI and GISAID submission requirements to PHA4GE field mappings 	| Many PHA4GE fields have been sourced from public repository submission requirements. The different repositories have different requirements and field names. Repository submission fields have been mapped to PHA4GE fields to demonstrate equivalencies and divergences. 	|  	|
 | [PHA4GE SARS-CoV-2 NCBI submission protocol- SRA, BioSample, and BioProject.pdf](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20NCBI%20submission%20protocol-%20SRA%2C%20BioSample%2C%20and%20BioProject.pdf), [SARS-CoV-2 NCBI assembly submission protocol: GenBank.pdf](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20NCBI%20assembly%20submission%20protocol-%20GenBank.pdf) and [PHA4GE SOP for populating NCBI submission templates for SARS-CoV-2 (BioSample, SRA, and GenBank).pdf](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SOP%20for%20populating%20NCBI%20submission%20templates%20for%20SARS-CoV-2%20(BioSample%2C%20SRA%2C%20and%20GenBank).pdf) | Data submission protocol (NCBI) 	| The SARS-CoV-2 submission protocol for NCBI provides step-by-step instructions and recommendations aimed at improving interoperability and consistency of submitted data. 	|  	|
-| [PHA4GE SARS-CoV-2 EBI submission protocol- ENA, BioSample, and BioProject.pdf](), [PHA4GE SARS-CoV-2 EBI assembly submission protocol.pdf]() and [PHA4GE SOP for populating EBI submission templates (ENA).pdf]()	| Data submission protocol (ENA) 	| The SARS-CoV-2 submission protocol for ENA provides step-by-step instructions and recommendations aimed at improving interoperability and consistency of submitted data. 	|  	|
+| [PHA4GE SARS-CoV-2 EBI submission protocol- ENA, BioSample, and BioProject.pdf](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20EBI%20submission%20protocol-%20ENA%2C%20BioSample%2C%20and%20BioProject.pdf), [PHA4GE SARS-CoV-2 EBI assembly submission protocol.pdf](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20EBI%20assembly%20submission%20protocol.pdf) and [PHA4GE SOP for populating EBI submission templates (ENA).pdf](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SOP%20for%20populating%20EBI%20submission%20templates%20(ENA).pdf)	| Data submission protocol (ENA) 	| The SARS-CoV-2 submission protocol for ENA provides step-by-step instructions and recommendations aimed at improving interoperability and consistency of submitted data. 	|  	|
 | [PHA4GE SARS-CoV-2 GISAID Submission Protocol](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20GISAID%20Submission%20Protocol.pdf) 	| Data submission protocol (GISAID)	| The SARS-CoV-2 submission protocol for GISAID provides step-by-step instructions and recommendations aimed at improving interoperability and consistency of submitted data. 	|  	|
 | [PHA4GE SARS-CoV-2 Standardised Terms.csv](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Standardised%20Terms.csv) and [PHA4GE_SARS-CoV-2_Contextual_Data_Schema.json](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE_SARS-CoV-2_Contextual_Data_Schema.json) 	| JSON structure of PHA4GE specification 	| A JSON structure of the PHA4GE specification has been provided for easier integration into software applications. Originated from the standardised terms csv file.	|  	|
 
 ### Collection template and controlled vocabulary pick lists
-The PHA4GE SARS-CoV-2 Contextual data Collection Template can be used for data management, and consists a 
-spreadsheet-based (.xlsx) collection template, a reference guide, and a controlled vocabulary list. This information 
-does not have to be shared, but sharing with public repositories is encouraged when permitted. 
+The [PHA4GE SARS-CoV-2 Contextual data Collection Template](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template.xlsx) 
+can be used for data management, and consists a spreadsheet-based (.xlsx) collection template, a reference guide, and a 
+controlled vocabulary list. This information does not have to be shared, but sharing with public repositories is 
+encouraged when permitted. 
 
 Fields are grouped according to whether they describe sampling, host information (symptoms, exposures etc), sequencing, 
 bioinformatics and quality control metrics, etc. The collection template contains "required" (colour-coded yellow), 
 "strongly recommended" (colour-coded purple) and "optional" (colour-coded white) fields. In many fields, picklists of 
 ontology-mapped controlled vocabulary are offered to better standardize data values. 
 
 ### Reference guide
-To facilitate the use of the collection template, a reference guide with field definitions, further 
-guidance/instructions, and examples of structured data is available.
+Available in the The [PHA4GE SARS-CoV-2 Contextual data Collection Template](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template.xlsx),
+the reference guide aims to facilitate the use of the collection template. It contains field definitions, further 
+guidance/instructions, and examples of structured data.
 
 ### Collection template SOP
-A Standard Operating Procedure (SOP) containing instructions for using the collection template. 
+A [Standard Operating Procedure (SOP)](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20Contextual%20Data%20SOP.docx) containing instructions for using the collection template. 
 
 The template SOP provides users with step-by-step instructions for populating the template, looking up standardized 
 terms, and how best to structure sample descriptions. The SOP also highlights a number of ethical, practical, and 
 privacy considerations for data sharing.
 
 ### PHA4GE fields to metadata standards mapping 
-Minimum information checklists are community standards that describe attributes of genomes in a standardized way. There are several existing standards that are useful for structuring SARS-CoV-2 contextual data. The PHA4GE SARS-CoV-2 specification implements these standards, and maps to standardized fields where applicable. Mapping of PHA4GE fields to the Sample Application Standard, MIxS v 5.0, and the MIGS Virus Host-associated package can be found in the reference guide. 
+Minimum information checklists are community standards that describe attributes of genomes in a standardized way. 
+There are several existing standards that are useful for structuring SARS-CoV-2 contextual data. 
+The PHA4GE SARS-CoV-2 specification implements these standards, and maps to standardized fields where applicable. 
+Mapping of PHA4GE fields to the Sample Application Standard, MIxS v 5.0, and the MIGS Virus Host-associated package can 
+be found in the [reference guide](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Contextual%20Data%20Template.xlsx). 
 
 
 ### ENA, NCBI and GISAID submission requirements to PHA4GE field mappings
@@ -91,11 +97,11 @@ The NCBI data submission process is covered by three separate protocols:
 ### Data submission protocol (ENA) 
 The data submission process is split into three separate protocols. 
 
-* [PHA4GE SOP for populating the three templates for SARS-CoV-2 submission to EBI]()
+* [PHA4GE SOP for populating the three templates for SARS-CoV-2 submission to EBI](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SOP%20for%20populating%20EBI%20submission%20templates%20(ENA).pdf)
     * **The protocol is available in protocols.io under the DOI [dx.doi.org/10.17504/protocols.io.bh5dj826](https://dx.doi.org/10.17504/protocols.io.bh5dj826).**
-* [PHA4GE SARS-CoV-2 EBI submission protocol for Biosamples and seqeuence read data]()
+* [PHA4GE SARS-CoV-2 EBI submission protocol for Biosamples and seqeuence read data](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20EBI%20submission%20protocol-%20ENA%2C%20BioSample%2C%20and%20BioProject.pdf)
     * **The protocol is available in protocols.io under the DOI [dx.doi.org/10.17504/protocols.io.bhwdj7a6](https://dx.doi.org/10.17504/protocols.io.bhwdj7a6).**
-* [PHA4GE SARS-CoV-2 EBI submission protocol for genome assemblies]()
+* [PHA4GE SARS-CoV-2 EBI submission protocol for genome assemblies](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20EBI%20assembly%20submission%20protocol.pdf)
     * **The protocol is available in protocols.io under the DOI [dx.doi.org/10.17504/protocols.io.bhwqj7dw](https://dx.doi.org/10.17504/protocols.io.bhwqj7dw).**
 
 ### Data submission protocol (GISAID)
@@ -110,7 +116,10 @@ limitation, it deviates slightly from the collection template where the "require
 set as required and both the "strongly recommended" (colour-coded purple) and "optional" (colour-coded white) fields 
 are both set as option. 
 
-The JSON is produced automatically from the [csv version](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Standardised%20Terms.csv) of the template using the [this](https://github.com/pha4ge/SARS-CoV-2-Data-Spec-JSON) script.
+The [JSON](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE_SARS-CoV-2_Contextual_Data_Schema.json) 
+is produced automatically from the [csv version](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Standardised%20Terms.csv) 
+of the template using the the script available from [SARS-CoV-2-Data-Spec-JSON](https://github.com/pha4ge/SARS-CoV-2-Data-Spec-JSON) 
+repository.
 
 **Table 2** Terms for SARS-CoV-2 submission template according to the PHA4GE contextual data collection specification in 
 [PHA4GE SARS-CoV-2 Standardised Terms](https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE%20SARS-CoV-2%20Standardised%20Terms.csv)  
