Hyperlink DOIs against preferred resolver

README.md

@@ -15,9 +15,9 @@ Currently, DATS is being used and further refined under the new phase of the [NI
 
 ## Publications
 - Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu; DataMed – an open source discovery index for finding biomedical datasets, Journal of the American Medical Informatics Association, Volume 25, Issue 3, 1 March 2018, Pages 300–308, https://doi.org/10.1093/jamia/ocx121
-- Alejandra N Gonzalez-Beltran, John Campbell, Patrick Dunn, Diana Guijarro, Sanda Ionescu, Hyeoneui Kim, Jared Lyle, Jeffrey Wiser, Susanna-Assunta Sansone, Philippe Rocca-Serra; **Data discovery with DATS: exemplar adoptions and lessons learned**, *Journal of the American Medical Informatics Association*, Volume 25, Issue 1, 1 January 2018, Pages 13–16, [http://doi.org/10.1093/jamia/ocx119]( http://doi.org/10.1093/jamia/ocx119)
-- Lucila Ohno-Machado, Susanna-Assunta Sansone, George Alter, Ian Fore, Jeffrey Grethe, Hua Xu, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Anupama E Gururaj, Elizabeth Bell, Ergin Soysal, Nansu Zong & Hyeon-eui Kim; **Finding useful data across multiple biomedical data repositories using DataMed**; *Nature Genetics* 49, 816–819 (2017) [http://doi.org/10.1038/ng.3864](http://doi.org/10.1038/ng.3864)
-- Susanna-Assunta Sansone<sup>#</sup>, Alejandra Gonzalez-Beltran<sup>#</sup>, Philippe Rocca-Serra<sup>#</sup>, George Alter, Jeffrey S. Grethe, Hua Xu, Ian M. Fore, Jared Lyle, Anupama E. Gururaj, Xiaoling Chen, Hyeon-eui Kim, Nansu Zong, Yueling Li, Ruiling Liu, I. Burak Ozyurt & Lucila Ohno-Machado; **DATS, the data tag suite to enable discoverability of datasets**; Scientific Data volume 4, Article number: 170059 (2017) [DOI: 10.1038/sdata.2017.59](http://doi.org/10.1038/sdata.2017.59) <sup>#</sup>=equal contribution; Pre-print: [bioRxiv DOI: 10.1101/103143 ](https://doi.org/10.1101/103143).
+- Alejandra N Gonzalez-Beltran, John Campbell, Patrick Dunn, Diana Guijarro, Sanda Ionescu, Hyeoneui Kim, Jared Lyle, Jeffrey Wiser, Susanna-Assunta Sansone, Philippe Rocca-Serra; **Data discovery with DATS: exemplar adoptions and lessons learned**, *Journal of the American Medical Informatics Association*, Volume 25, Issue 1, 1 January 2018, Pages 13–16, [https://doi.org/10.1093/jamia/ocx119]( https://doi.org/10.1093/jamia/ocx119)
+- Lucila Ohno-Machado, Susanna-Assunta Sansone, George Alter, Ian Fore, Jeffrey Grethe, Hua Xu, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Anupama E Gururaj, Elizabeth Bell, Ergin Soysal, Nansu Zong & Hyeon-eui Kim; **Finding useful data across multiple biomedical data repositories using DataMed**; *Nature Genetics* 49, 816–819 (2017) [https://doi.org/10.1038/ng.3864](https://doi.org/10.1038/ng.3864)
+- Susanna-Assunta Sansone<sup>#</sup>, Alejandra Gonzalez-Beltran<sup>#</sup>, Philippe Rocca-Serra<sup>#</sup>, George Alter, Jeffrey S. Grethe, Hua Xu, Ian M. Fore, Jared Lyle, Anupama E. Gururaj, Xiaoling Chen, Hyeon-eui Kim, Nansu Zong, Yueling Li, Ruiling Liu, I. Burak Ozyurt & Lucila Ohno-Machado; **DATS, the data tag suite to enable discoverability of datasets**; Scientific Data volume 4, Article number: 170059 (2017) [DOI: 10.1038/sdata.2017.59](https://doi.org/10.1038/sdata.2017.59) <sup>#</sup>=equal contribution; Pre-print: [bioRxiv DOI: 10.1101/103143 ](https://doi.org/10.1101/103143).
 
 ## DATS Releases
 
@@ -28,26 +28,26 @@ All DATS releases can be accessed in Zenodo through the [DATS Community](https:/
 * [DATS model version 2.2 (Google Document)](https://docs.google.com/document/d/1hVcYRleE6-dFfn7qbF9Bv1Ohs1kTF6a8OwWUvoZlDto/edit?usp=sharing)
 
 
-### Version 2.1 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.62024.svg)](http://dx.doi.org/10.5281/zenodo.62024)
+### Version 2.1 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.62024.svg)](https://doi.org/10.5281/zenodo.62024)
 
 The document provides links to the different appendices files.
 
 * [DATS model version 2.1 (pdf)](https://github.com/biocaddie/WG3-MetadataSpecifications/blob/master/doc/v2.1/DataMedDATSspecificationv2.1-NIH-BD2KbioCADDIE.pdf)
 
 
 
-### Version 2.0 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.54010.svg)](http://dx.doi.org/10.5281/zenodo.54010)
+### Version 2.0 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.54010.svg)](https://doi.org/10.5281/zenodo.54010)
 
 The document provides links to the different appendices files.
 
 * [DATS model version 2.0 (pdf)](https://github.com/biocaddie/WG3-MetadataSpecifications/blob/master/doc/v2.0/DataMedDATSspecificationv2-NIHDB2KbioCADDIE.pdf)
 
-### Version 1.1 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.53078.svg)](http://dx.doi.org/10.5281/zenodo.53078)
+### Version 1.1 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.53078.svg)](https://doi.org/10.5281/zenodo.53078)
 
 
 * [Metadata Specification - version 1.1 - Draft open for comments (doc)] (https://github.com/biocaddie/WG3-MetadataSpecifications/blob/master/doc/v1.1/NIH-BS2K-bioCADDIE-WG3-MetadataElements-Specification-v1.1.docx) 
 
-### Version 1.0 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.28019.svg)](http://dx.doi.org/10.5281/zenodo.28019)
+### Version 1.0 - [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.28019.svg)](https://doi.org/10.5281/zenodo.28019)
 
 
 * [Metadata Specification - version 1.0 (PDF file)](https://github.com/biocaddie/WG3-MetadataSpecifications/blob/master/doc/v1.0/WG3MetadataSpecificationv1-NIH-BD2K-bioCADDIE-DataDiscoveryIndex.pdf)

docs/source/index.rst

@@ -13,7 +13,7 @@ DATS, which stands for DAta Tag Suite, is a data description model designed and
 
 For more information about DATS, please check the DATS pre-print available in `bioarxiv <https://doi.org/10.1101/103143>`_.
 For more information about DataMed, please check the DataMed pre-print available in `bioarxiv <https://doi.org/10.1101/094888>`_.
-For more information about the objectives of the bioCADDIE project, please have a look at the `bioCADDIE White Paper <https://dx.doi.org/10.6084/m9.figshare.1362572.v1>`_.
+For more information about the objectives of the bioCADDIE project, please have a look at the `bioCADDIE White Paper <https://doi.org/10.6084/m9.figshare.1362572.v1>`_.
 
 
 This documentation describes the DATS model and how to use it. More details about how DATS was designed and how it relates to other models can be found in the aforementioned documents as well as in the `documents accompanying each of the releases <https://github.com/biocaddie/WG3-MetadataSpecifications/tree/master/doc>`_.

json-instances/ClinicalTrials.gov-NCT00001372.json

@@ -48,7 +48,7 @@
       },
       "alternateIdentifiers": [
         {
-         "identifier": "http://dx.doi.org/10.7326/0003-4819-123-1-199507010-00007",
+         "identifier": "https://doi.org/10.7326/0003-4819-123-1-199507010-00007",
           "identifierSource": "doi"
         }
       ],

json-instances/ICPSR-33581/DatasetDistribution-33581.json

@@ -34,7 +34,7 @@
 					"value": "dualInstitution"
 				}
 			],
-			"landingPage": "http://doi.org/10.3886/ICPSR06849.v1",
+			"landingPage": "https://doi.org/10.3886/ICPSR06849.v1",
 			"types": [
 				{
 					"ontologyTermIRI": "",
@@ -105,4 +105,4 @@
 		} 
 	], 
 	"size": 1817203948721
-}
+}

json-instances/NYU-10040-dats.json

@@ -273,7 +273,7 @@
   "primaryPublications": [
     {
       "identifier": {
-        "identifier": "https://dx.doi.org/10.1186%2F1745-6215-13-126",
+        "identifier": "https://doi.org/10.1186%2F1745-6215-13-126",
         "identifierSource": "doi"
       },
       "alternateIdentifiers": [
@@ -712,4 +712,4 @@
       }
     }
   ]
-}
+}