.. reproducible research tutorial file, created by ARichards

============
Data Sharing
============

In order to reproduce a study the data used to create the figures and the data used as input for the statistical methods are **required**. `Data sharing <http://en.wikipedia.org/wiki/Data_sharing>`_ is one of the most challenging aspects of reproducible research, because in many fields the tendency has been to hold on the data for as long as possible.  Data sharing can also refer to resource sharing meaning: the reagents, buffers, cell lines and just about anything else necessary to carry out an experiment.  Our focus on the `raw data <http://en.wikipedia.org/wiki/Raw_data>`_ and as associated `metadata <http://en.wikipedia.org/wiki/Metadata>`_, though the scientific process is helped, by offering to share additional material aspects of experiments.

Fortunately, there are many efforts, some decades in the making, that facilitate data sharing.  The following are links and resources meant to aid researchers in their effort to share data.  An important aspect of the listed resources is that they are all free for general scientific use.

General Web resources
^^^^^^^^^^^^^^^^^^^^^

  * `NCBI <www.ncbi.nlm.nih.gov/>`_ - The National Center for Biotechnology Information
  * `EMBL-EBI <http://www.ebi.ac.uk/>`_ - The European Bioinformatics Institute
  * `biosharing.org <http://biosharing.org>`_ - A resource for databases and reporting standards in biology.

Repositories
^^^^^^^^^^^^
  
  * `GenBank <http://www.ncbi.nlm.nih.gov/genbank/>`_ - The central resource for gene information
  * `UniProt <http://www.uniprot.org/>`_ - The protein knowledgebase (SwissProt and TrEMBL).
  * `SwissProt <http://web.expasy.org/docs/swiss-prot_guideline.html>`_ - Curated protein database
  * `GEO <http://www.ncbi.nlm.nih.gov/geo/>`_ - The Gene Expression Omnibus is a repository for functional genomics data.
  * `ArrayExpress <http://www.ebi.ac.uk/arrayexpress/>`_ - Another database for functional genomics experiments
  * `PubMed <http://www.ncbi.nlm.nih.gov/pubmed>`_. - Citations from the biomedical literature 

Reporting standards
^^^^^^^^^^^^^^^^^^^

  * `RNAseq standards report from encode (pdf) <http://genome.ucsc.edu/ENCODE/protocols/dataStandards/ENCODE_RNAseq_Standards_V1.0.pdf>`_
  * `MIAME standards <http://www.ncbi.nlm.nih.gov/geo/info/MIAME.html>`_ - for microarray experiments
  * `MINSEQE standards <http://www.fged.org/projects/minseqe/>`_ - for high-throughput sequencing experiments
  * `GIS stantards <http://www.ecy.wa.gov/services/gis/data/standards/standards.htm>`_ - creating and accessing GIS data

Interesting Articles
^^^^^^^^^^^^^^^^^^^^^^^

  * `Nine simple ways to make it easier to (re)use your data (pdf) <https://peerj.com/preprints/7.pdf>`_
  * `NIH perspective on data sharing <http://grants.nih.gov/grants/policy/data_sharing/data_sharing_faqs.htm>`_