\name{PFAMCAZY}
\alias{PFAMCAZY}
\alias{PFAMDE}
\alias{PFAMID}
\alias{PFAMHOMSTRAD}
\alias{PFAMINTERPRO}
\alias{PFAMLOAD}
\alias{PFAMMEROPS}
\alias{PFAMMIM}
\alias{PFAMPRINTS}
\alias{PFAMPROSITE}
\alias{PFAMPROSITEPROFILE}
\alias{PFAMRM}
\alias{PFAMSMART}
\alias{PFAMTC}
\alias{PFAMTP}
\alias{PFAMURL}

\title{Mappings from a PFAM Accession number to another kind of ID}
\description{
  This is an R object that always contains mappings from a PFAM ID to the
  other ID type named by the object
}
\details{
  For each of the aliases listed above, there is a mapping object that
  corresponds which will map you from the appropriate PFAM accession
  number to the ID type that is in the environments name.  So for
  example PFAMCAZY will map from PFAM IDs to CAZY IDs while
  PFAMDE will map from PFAM IDs to Descriptions.

  CAZY: The CAZy database (<URL: http://afmb.cnrs-mrs.fr/CAZY/>)
     describes the families of structurally-related catalytic and
     carbohydrate-binding modules (or functional domains) of enzymes
     that degrade, modify, or create glycosidic bonds.
     
  DE:  Definition for all the Accession number in the database.

  ID:  Associated Identification for all the Accession number in the
     database.

  HOMSTRAD:  HOMSTRAD (HOMologous STRucture Alignment Database, <URL:
     http://www-cryst.bioc.cam.ac.uk/homstrad/>) is a curated database
     of structure-based alignments for homologous protein families.
     Reference: Mizuguchi K, Deane CM, Blundell TL, Overington JP.
     (1998) HOMSTRAD: a database of protein structure alignments for
     homologous families. Protein Science 7:2469-2471.

  INTERPRO:  Associated INTERPRO ID for all the Accession number in the
     database.  <URL: http://www.ebi.ac.uk/interpro/> 

  LOAD:  LOAD ID for all the Accession number in the database.

  MEROPS:  The MEROPS database (<URL: http://merops.sanger.ac.uk/>) is
     an information resource for peptidases (also termed proteases,
     proteinases and proteolytic enzymes) and the proteins that inhibit
     them. Reference: Rawlings, N.D., Tolle, D.P. & Barrett, A.J. (2004)
     MEROPS: the peptidase database. Nucleic Acids Res. 32 Database
     issue, D160-D164

  MIM:  MIM (a.k.a. OMIM, <URL: https://www.ncbi.nlm.nih.gov/omim/>) is a
     catalog of human genes and genetic disorders authored and edited by
     Dr. Victor A. McKusick and his colleagues at Johns Hopkins and
     elsewhere. Reference:  <MIM> MIM: McKusick, V.A.: Mendelian
     Inheritance in Man. A Catalog of Human Genes and Genetic
     Disorders. Baltimore: Johns Hopkins University Press, 1998 (12th
     edition). <OMIM> Online Mendelian Inheritance in Man, OMIM
     (TM). McKusick-Nathans Institute for Genetic Medicine, Johns
     Hopkins University (Baltimore, MD) and National Center for
     Biotechnology Information, National Library of Medicine (Bethesda,
     MD), 2000


  PRINTS:  PRINTS (<URL: http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/>)
    is a compendium of protein fingerprints.

  PROSITEPROFILE:  A list of associated PROSITE PROFILE ID.

  RM:  Reference Medline (<URL: https://www.ncbi.nlm.nih.gov/PubMed/>)

  SMART:  SMART (a Simple Modular Architecture Research Tool, <URL:
    http://smart.embl-heidelberg.de/>) allows the identification and
    annotation of genetically mobile domains and the analysis of domain
    architectures.  Reference: (1) Schultz et al. (1998)
    Proc. Natl. Acad. Sci. USA 95, 5857-5864.  (2) Letunic et al. (2004)
    Nucleic Acids Res 32, D142-D144

  TC:  Trusted cutoff for all the Accession number in the database.

  TP:  A list of associated Type field for the given Accession.

  URL:  A list of associated URL for all the Accession number in the
    database.
  
}

\references{
  \url{http://www.sanger.ac.uk/Software/Pfam/} and
  \url{ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt}
}

\seealso{
  \itemize{
    \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of
          the \code{select()} interface.
  }
}

\examples{
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
#To map from PFAM to CAZYs:
x <- PFAMCAZY
# Get the PFAM identifiers that are mapped to a CAZY
mapped_keys <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_keys])
if(length(xx) > 0) {
  # Get the CAZY for the first five PFAM IDs
  xx[1:5]
  # Get the first one
  xx[[1]]
}

#Or to use the DE mapping:
x <- PFAMDE
# Get the PFAM identifiers that are mapped to a DE
mapped_keys <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_keys])
if(length(xx) > 0) {
  # Get the DE for the first five PFAM IDs
  xx[1:5]
  # Get the first one
  xx[[1]]
}

#etc.
}
\keyword{datasets}
