\name{PFAMCAZY2AC}
\alias{PFAMCAZY2AC}
\alias{PFAMDE2AC}
\alias{PFAMID2AC}
\alias{PFAMHOMSTRAD2AC}
\alias{PFAMINTERPRO2AC}
\alias{PFAMLOAD2AC}
\alias{PFAMMEROPS2AC}
\alias{PFAMMIM2AC}
\alias{PFAMPRINTS2AC}
\alias{PFAMPROSITE2AC}
\alias{PFAMPROSITEPROFILE2AC}
\alias{PFAMRM2AC}
\alias{PFAMSMART2AC}
\alias{PFAMTC2AC}
\alias{PFAMTP2AC}
\alias{PFAMURL2AC}

\title{Mappings from an ID to a PFAM Accession number}
\description{
  This is an R object that contains mapppings from an ID to its
  PFAM Accession number (AC)
}
\details{
  For each of the aliases listed above, there is a mapping object that
  corresponds which will map you from the ID type in the environments
  name to the appropriate PFAM accession number.  So for example
  PFAMCAZY2AC will map from CAZY IDs to PFAM IDs while
  PFAMDE2AC will map from Descriptions to PFAM IDs.

  Details on supported things that are mapped to:

  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 CAZY to PFAM IDs:
x <- PFAMCAZY2AC
# Get the CAZY identifiers that are mapped to a PFAM ID
mapped_keys <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_keys])
if(length(xx) > 0) {
  # Get the PFAM ID for the first five CAZYs
  xx[1:5]
  # Get the first one
  xx[[1]]
}

#Or to use the DE2AC mapping:
x <- PFAMDE2AC
# Get the Descriptions that are mapped to a PFAM ID
mapped_keys <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_keys])
if(length(xx) > 0) {
  # Get the PFAM ID for the first five DEs
  xx[1:5]
  # Get the first one
  xx[[1]]
}
}

\keyword{datasets}
