Copyright (C) 2020 University of Southern California

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

############################################################################
README for PANTHER HMM Classifications
http://www.pantherdb.org
Last updated: Februrary, 2020
------------

This file contains the name, molecular functions, biological processes, and pathway for every PANTHER protein family and subfamily in Version 15.0 of the PANTHER HMM library.  The current Pathway release is version 3.6.4.


The file is a tab-delimited file in the following format:
1) PANTHER ID:  for example, PTHR11258 or PTHR12213:SF6.  ":SF" indicates the subfamily ID
2) Name:  The annotation assigned by curators to the PANTHER family or subfamily
3) Molecular function*:  PANTHER GO slim molecular function terms assigned to families and subfamilies
4) Biological process*:  PANTHER GO slim biological process terms assigned to families and subfamilies
5) Cellular components*:  PANTHER GO slim cellular component terms assigned to families and subfamilies
6) Protein class*  PANTHER protein class terms assigned to families and subfamilies
7) Pathway***: PANTHER pathways have been assigned to families and subfamilies.  


*Example Molecular function (the same format applies to biological process, cellular component and protein class)
transferase activity#GO:0016740;enzyme regulator activity#GO:0030234;protein binding#GO:0005515


The term accessions are listed after the # sign.  Each term is separated by a semicolon.  Unlike in previous version, only the terms assigned to the families or subfamilies are listed.  The "parent" categories are not listed in this release.

***Example Pathway:
Inflammation mediated by chemokine and cytokine signaling pathway#Inflammation mediated by chemokine and cytokine signaling pathway#P00031>Integrin#Integrin#P00853;Integrin signalling pathway#Integrin signalling pathway#P00034>Integrin  alpha#Integrin alpha#P00941

The format of the pathway information is: pathway_long_name#pathway_short_name#pathway_accession>component_long_name#component_short_name#component_accession


Explanation of pathway accessions:
Gxxxxx   Gene or RNA
Pxxxxx   Protein
Sxxxxx   small molecules
Uxxxxx   others, such as "unknown", etc.

If you have any questions, please contact us at: feedback@pantherdb.org

-----

Version History

February 14, 2020 - PANTHER 15.0
March 20, 2019 - PANTHER 14.1
December 19, 2018 - PANTHER 14.0
December 19, 2018 - PANTHER pathway 3.6.2
October 24, 2017 - PANTHER 13.0
October 24, 2017 - PANTHER pathway 3.6
January 15, 2014 - PANTHER 9.0
January 15, 2014 - PANTHER pathway 3.1
May 15, 2013 - PANTHER 8.1
May 15, 2013 - PANTHER pathway 3.2
March 15, 2012 - PANTHER 7.2
March 15, 2012 - PANTHER pathway 3.1
March 30, 2010 - PANTHER Pathway 3.0
March 30, 2010 - PANTHER7.0
February 22, 2008 - PANTHER Pathway 2.1
December 8, 2006 - PANTHER6.1
September 29, 2006 - update to fix bug where some subfamilies had tabs in the subfamily name
July 20, 2006 - update for PANTHER Pathway Version 1.3.  Also, there was missing data in the original release, and this has now been fixed
February 16, 2006 - original release