Data
=====

The top-level Data Menu provides direct access to data sets by type or special grouping within PATRIC.

.. image:: ../images/data_menu.png

Clicking on one of the items on the main PATRIC header menu will display the corresponding summary-level page here in PATRIC's documentation.

Data Types
-----------
The Data Types submenu items link to summary information pages that provide descriptions and as well as linked examples for the various data elements in PATRIC, along with how we derive, curate, map, and/or integrate the data of that type.

.. toctree::
   :maxdepth: 1

   data_types/antimicrobial_resistance
   data_types/genomes
   data_types/genomic_features
   data_types/pathways
   data_types/protein_families
   data_types/specialty_genes
   data_types/transcriptomics

Specialty Data Collections
--------------------------
The Specialty Data Collections submenu items link to pages in PATRIC featuring data sets of interest that are related either by collaborations, common programs (e.g., NIAID-funded centers), or other grouping.  Summaries, experimental information, and links to data sets and corresponding publications are provided.  Where appropriate, the data sets have been integrated into PATRIC.

.. toctree::
   :maxdepth: 1

   specialty_data_collections/patric_collaborations
   specialty_data_collections/patric_dbps
   specialty_data_collections/niaid_clinical_proteomics
   specialty_data_collections/niaid_genome_sequencing
   specialty_data_collections/niaid_structural_genomics
   specialty_data_collections/niaid_systems_biology
   specialty_data_collections/niaid_functional_genomics

Download Data
-------------

Access |ftp_link|.

.. |ftp_link| raw:: html

  <a href="ftp://ftp.patricbrc.org/" target="_blank">PATRIC FTP Server</a><br>
  (opens in a new tab)