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added LICENSE file, message in zzz.R, and updated DESCRIPTION accordingly

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotifDb@76942 bc3139a8-67e5-0310-9ffc-ced21a209358

p.shannon authored on 28/05/2013 21:13:28
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.3.8
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-Date: 2013-04-09
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+Version: 1.3.9
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+Date: 2013-05-28
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 Author: Paul Shannon
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 Maintainer: Paul Shannon <pshannon@fhcrc.org>
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 Depends: R (>= 2.15.0), methods, IRanges, Biostrings
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 Suggests: RUnit, MotIV, seqLogo
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 Imports: BiocGenerics, rtracklayer
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 Description: More than 2000 annotated position frequency matrices from five public source, for multiple organisms
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-License: Artistic-2.0
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+License: Artistic-2.0 | file LICENSE
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+License_is_FOSS: no
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+License_restricts_use: yes
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 LazyLoad: yes
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 biocViews: GenomicSequence, MotifAnnotation
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new file mode 100644
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+Bioconductor Package MotifDb: LICENSE
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+
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+MotifDb is a collection of position weight matrices and metadata obtained
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+from six sources, with some restriction upon commercial use as described
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+below:
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+
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+| 2769 position frequency matrices from 6 sources:
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+|    FlyFactorSurvey:  614
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+|        JASPAR_CORE:  459
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+|             ScerTF:  196
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+|           UniPROBE:  380
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+|               hPDI:  437
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+|            stamlab:  683
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+
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+FlyFactorSurvey:  all data described as "public"
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+[http://pgfe.umassmed.edu/ffs/DownloadData.php]
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+
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+JASPAR_CORE:  "The JASPAR CORE database contains a curated,
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+non-redundant set of profiles, derived from published collections of
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+experimentally defined transcription factor binding sites for
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+eukaryotes. The prime difference to similar resources (TRANSFAC, etc)
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+consist of the open data acess, non-redundancy and quality."
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+  [http://jaspar.genereg.net/]
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+
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+ScerTF: "The entire database of optimal matrices selected for all S.
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+cerevisiae transcription factors is available for download here."  No
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+restrictions mentioned.   Spivak and Stormo explain that they curated
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+their collection from ten sources, listed here:
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+http://stormo.wustl.edu/ScerTF/download/.
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+
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+UniPROBE: "Please note that any files which contain PBM probe sequences
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+are protected by an academic research use license, which will require
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+confirmation prior to file download." (from ).  I exchanged email with
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+Martha Bulyk and her staff in May 2012, explained the MotifDb project,
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+they were helpful.  I will check my import code to see whether I use
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+their PBM probe sequences.
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+
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+hPDI:  "The content in the hPDI database is free to academic and
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+non-profit organizations. Users for commercial purpose please contact
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+the authors before download the data sets."
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+
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+stamlab: These motifs are part of the ENCODE project, and (I assume) public.
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@@ -22,6 +22,8 @@ MotifDb <- NULL
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       }
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     } # if loadAllSources
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+   message('See system.file("LICENSE", package="MotifDb") for use restrictions.')
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+  
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   return(mdb)
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 } # MotifDb