Merge pull request #639 from isb-cgc/staging

Staging

docs/source/index.rst

@@ -44,6 +44,7 @@ The `ISB-CGC <https://isb-cgc.org>`_ aims to serve the needs of a broad range of
    sections/DataExplorer
    sections/DataBrowser
    sections/data/Mitelman_about
+   sections/the_TP53_database
    sections/ProgrammaticAccess
    sections/data/TCGA_Data_Security
    sections/Gaining-Access-To-Controlled-Access-Data 

docs/source/sections/the_TP53_database.rst

@@ -0,0 +1,49 @@
+***********************
+The *TP53* Database
+***********************
+
+The *TP53* Database (`<https://tp53.isb-cgc.org>`_) compiles *TP53* variant data that have been reported in the published literature since 1989 or are available in other public databases. `Database releases <https://tp53.isb-cgc.org/about#database-dev-div>`_ are identified by a number.
+The following data are available:
+
+- *TP53* `functional and structural data <https://tp53.isb-cgc.org/explore_gv>`_ including `validated polymorphisms <https://tp53.isb-cgc.org/view_val_poly>`_
+- *TP53* `somatic variants <https://tp53.isb-cgc.org/explore_sm>`_ in sporadic cancers
+- *TP53* `germline variants <https://tp53.isb-cgc.org/explore_gm>`_ in cancer patients, families with cancers and control populations
+- *TP53* `gene status in human cell-lines <https://tp53.isb-cgc.org/explore_cl>`_
+- `Mouse models <https://tp53.isb-cgc.org/explore_mm>`_ with engineered p53
+- `Experimentally-induced variants <https://tp53.isb-cgc.org/explore_eim>`_ of *TP53*
+
+The *TP53* Database is meant to be a source of information on *TP53* variants for a broad range of scientists and clinicians who work in different research areas:
+
+- **Basic research**, to study the structural and functional aspects of the p53 protein and the *TP53* gene
+- **Molecular pathology of cancer**, to understand the clinical significance of *TP53* variants identified in cancer patients
+- **Molecular epidemiology of cancer**, to analyze the links between specific exposures and *TP53* variant patterns in order to make inferences about possible causes of cancer
+- **Molecular genetics**, to analyze genotype/phenotype relationships
+
+The database includes various annotations on the predicted or experimentally assessed functional impact of *TP53* variants, clinicopathologic characteristics of tumors
+and demographic and life-style information on patients. This information is useful to compile tumor-specific variant patterns and to draw hypotheses on the nature of the
+molecular events involved in *TP53* mutagenesis and allows for the analysis of genotype/phenotype relationships.
+
+Detailed information on data and annotations available is provided in the `User Manual <https://tp53.isb-cgc.org/help>`_.
+
+The ongoing project involves:
+
+- Performing regular review of the literature on *TP53* variants
+- Extracting *TP53* data from genetic and genomic databases
+- Developing standard annotations of *TP53* variants
+- Performing research on *TP53* variants, their patterns, origins and clinical impacts.
+
+How to Cite
+-----------
+
+When using the database, authors should cite the following source:
+
+  The *TP53* Database (R20, July 2019): https://tp53.isb-cgc.org 
+
+and refer to Bouaoun et al. in the bibliography as below:
+
+  Bouaoun L, Sonkin D, Ardin M, Hollstein M, Byrnes G, Zavadil J, Olivier M. *TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data*. Hum Mutat. 2016 Sep;37(9):865-76. doi: 10.1002/humu.23035. Epub 2016 Jul 8.
+
+More Information 
+----------------
+
+For information regarding releases, credits and disclaimers, please see the *TP53* `About <https://tp53.isb-cgc.org/about>`_ page.