_____ _
  / ____| |
 | |    | |__   __ _ _ __   __ _  ___  ___
 | |    | '_ \ / _` | '_ \ / _` |/ _ \/ __|
 | |____| | | | (_| | | | | (_| |  __/\__ \
  \_____|_| |_|\__,_|_| |_|\__, |\___||___/
                            __/ |
                           |___/

In this file we are outlining the various changes that have occurred in the
data stored on this FTP site.

---- May 2016 ------

PSI XML export changes :

 - Introducing PSI XML 3.0 format.
 - 3.0 format xmls are available in psi30 folder beside psi25 folder.
 - MIF300.xsd is available inside psi30 folder.
 - species xml, under psi30 species folder, naming convention has been changed as follows :-
   - The prefix "species name" has been changed to "species name"_"taxonomy id" ,
     the suffix convention :-
      1) For more than 2000 interactions, file are divided into multiple files each having 2000 interactions and convention is
         _fileno and for negative interactions _fileNo_negative
      2) For less than 2000
         only suffix is for negative interactions _negative.
 - As for psi25, in psi30 too species are splitted into smaller chunks, publications are no longer splitted into smaller sizes.
 - 3.0 complex xmls are kept inside respective species folder (naming convention of folder - "species short label" )
 - 3.0 complex xmls naming convention - "complex name".xml



---- 2012-10-16 ----

PSI MITAB export changes :

- intact-clustered.txt and intact-clustered.zip have been removed and replaced by intact-micluster.txt, intact-micluster_negative.txt, intact-micluster.zip. The intact-micluster is based on MITAB 2.5 and is using the MI cluster and scoring algorithm (http://code.google.com/p/micluster/).
- the intact publication files (pmid folder) are not clustered and based on MITAB 2.7 (http://code.google.com/p/psicquic/wiki/MITAB27Format). Negative interactions are exported in a separate file ending with '_negative'.
- pmidMITAB25.zip has been replaced by pmidMITAB2.7.zip

PSI XML export changes :

- intra-molecular interactions will now have a proper flag intraMolecular = true

---- 2011-10-24 ----

PSI XML export changes :

- psi1 is not supported anymore.

- Stoichiometry of a participant is now exported in the attributes of the
  participant (if available). The attribute containing the stoichiometry
  has a name comment and a value starting with 'Stoichiometry :'

- The interaction parameters and participant parameters are now exported
  when they are available

- The annotations of a participant are now exported in the attributeList of
  the participants when available.

- The confidences of a participant are now exported when available.

- The experimental preparations are now exported when available.

- The released date in the source of each publication XML file is now the date
  when the publication was released for the first time on the ftp site.

- A zip file is provided for each species in the species directory.
  Each zip file will contain all the xml files of a specic species.

- A species XML file can now contain more than one 'entry tag'.
  Each entry element will contain the experiments and interactions curated by
  a given institution (can be IntAct, Molecular Connections, InnateDB, etc.)
  so we don't loose the source informatio when merging several publications in
  a species file.


HOW DO WE SPLIT LARGE XML FILES?

- A large scale experiment containing more than 2000 interactions will be split
  in different xml file ending with the experiment label and a chunk number.
  In this case, each XML ending with the experiment short label will repeat
  the experiment decsription but all described interactions must be unique
  among the different files.

- When a publication or species reports more than 2000 interactions, we split
  the XML files in several chunks of 2000 interactions and each file ends with
  a chunk number. All interactions and experiments must be unique among the
  different files. We never split an experiment of less than 2000 interactions.

---- 2021-07-06 ----

- Html files to document the FTP structure have been replaced with plain text version
  to be able to use http:// and https:// protocols to navigate the FTP with a browser