[med-svn] r306 - trunk/community/debtags

Mon Jun 4 13:27:59 UTC 2007

Author: smoe-guest
Date: 2007-06-04 13:27:59 +0000 (Mon, 04 Jun 2007)
New Revision: 306

Modified:
   trunk/community/debtags/tags
Log:
Removed some prior nonsense of mine, brought the format
closer to what debtags might expect from us - you all 
please start editing descriptions.

Cheers,

Steffen



Modified: trunk/community/debtags/tags
===================================================================

--- trunk/community/debtags/tags	2007-06-04 12:42:39 UTC (rev 305)
+++ trunk/community/debtags/tags	2007-06-04 13:27:59 UTC (rev 306)
@@ -1,103 +1,211 @@
-field::biology:annotation
-field::biology:sequence
-field::biology:sequence:dna
-field::biology:sequence:rna
-field::biology:sequence:protein
-# I would rather move the :sequence tags to the works-with:: facet -- Charles
-field::biology:structural
-field::biology:molecular
-field::biology:evolution
-field::biology:interaction
-field::biology:genomics
-field::biology:proteomics
-field::biology:metabolomics
-field::biology:transcriptiomics
-field::biology:systems
-field::mathematics:graphs
-field::medicine:imaging
-field::medicine:practice
-field::medicine:odontology
-field::medicine:his
-hardware::input:dmm
-implemented-in::ACD # The AJAX Command Definition (ACD) languag, used by EMBOSS, has nothing to do with web 2.0
-suite::emboss # will also be used for the embassy pacakges
-use::annotation
-use::analysis # further depths would be redundant with the works-with:: facet
-use::comparison
-use::comparison:alignment
-use::comparison:phylogeny
-use::experiment
-use::experiment:molecular-biology
-use::measuring
-use::database:index # Or just use::index since there is already a works-with::db tag ?
-use::database:query # Or just use::query since there is already a works-with::db tag ?
-works-with::device
-works-with::sequence:desoxyribonucleic
-works-with::sequence:ribonucleic   # or just sequence:nucleic? 
-# I think that sequence:biolgical would be superfluous because of the field::biology tag
-works-with::sequence:peptidic
-works-with::structure              # or can it be unified with works-with::3Dmodel?
-works-with-format::abi		# Applied BIosystems. This one is not plaintext, I think.
-works-with-format::fitch        # neither this one
-works-with-format::biology:fasta
-works-with-format::biology:aln
-works-with-format::biology:pdb
-works-with-format::biology:embl
-works-with-format::biology:affy:dat
-works-with-format::biology:affy:cel
-# I would rather move the above formats in the ::plaintext subfacet -- Charles
-# This is fine with me. And what about affy:cdf? This could go to plaintext:cdf directly? -- Steffen
+Tag: field::biology:sequence
+Description: Biological sequence analysis
 
-works-with-format::plaintext:acedb
-works-with-format::plaintext:aln
-works-with-format::plaintext:asn1
-works-with-format::plaintext:codata
-works-with-format::plaintext:dbid
-works-with-format::plaintext:embl
-works-with-format::plaintext:experiment
-works-with-format::plaintext:fasta
-works-with-format::plaintext:gcg
-works-with-format::plaintext:gff
-works-with-format::plaintext:hennig86
-works-with-format::plaintext:ij
-works-with-format::plaintext:jackknifer
-works-with-format::plaintext:jackknifernon
-works-with-format::plaintext:mega
-works-with-format::plaintext:meganon
-works-with-format::plaintext:msf
-works-with-format::plaintext:nbrf
-works-with-format::plaintext:ncbi
-works-with-format::plaintext:nexus
-works-with-format::plaintext:nexusnon
-works-with-format::plaintext:paup
-works-with-format::plaintext:paupnon
-works-with-format::plaintext:pdb
-works-with-format::plaintext:pir
-works-with-format::plaintext:pfam
-works-with-format::plaintext:phylip
-works-with-format::plaintext:phylipnon
-works-with-format::plaintext:raw	#OK, that one advocates against the use of plaintext.
-works-with-format::plaintext:selex
-works-with-format::plaintext:staden
-works-with-format::plaintext:strider
-works-with-format::plaintext:stockholm
-works-with-format::plaintext:swissprot
-works-with-format::plaintext:treecon
-works-with-format::plaintext:affy:dat
-works-with-format::plaintext:affy:cel
-works-with-format::medicine:practice:xDT
-works-with-format::medicine:DICOM # or works-with-format::dicom ? -- Charles
+Tag: field::biology:sequence:dna
 
+Tag: field::biology:sequence:rna
+
+Tag: field::biology:sequence:protein
+
+Tag: # I would rather move the :sequence tags to the works-with:: facet -- Charles
+
+Tag: field::biology:structural
+
+Tag: field::biology:molecular
+
+Tag: field::biology:evolution
+
+Tag: field::biology:interaction
+
+Tag: field::biology:genomics
+
+Tag: field::biology:proteomics
+
+Tag: field::biology:metabolomics
+
+Tag: field::biology:transcriptiomics
+
+Tag: field::biology:systems
+
+Tag: field::mathematics:graphs
+
+
+Tag: field::medicine:imaging
+
+Tag: field::medicine:practice
+
+Tag: field::medicine:odontology
+
+Tag: field::medicine:his
+
+Tag: field::statistics:clustering
+
+Tag: field::statistics:classifyer
+
+Tag: hardware::input:dmm
+
+Tag: implemented-in::ACD # The AJAX Command Definition (ACD) languag, used by EMBOSS, has nothing to do with web 2.0
+
+Tag: suite::emboss # will also be used for the embassy pacakges
+
+Tag: use::annotation
+
+Tag: use::analysis # further depths would be redundant with the works-with:: facet
+
+Tag: use::comparison
+
+Tag: use::comparison:alignment
+
+Tag: use::comparison:phylogeny
+
+Tag: use::experiment
+
+Tag: use::experiment:molecular-biology
+
+Tag: use::measuring
+
+Tag: use::database:index # Or just use::index since there is already a works-with::db tag ?
+
+Tag: use::database:query # Or just use::query since there is already a works-with::db tag ?
+
+Tag: works-with::device
+
+Tag: works-with::sequence:desoxyribonucleic
+
+Tag: works-with::sequence:ribonucleic   # or just sequence:nucleic? 
+Tag: # I think that sequence:biolgical would be superfluous because of the field::biology tag
+
+Tag: works-with::sequence:peptidic
+
+Tag: works-with::structure              # or can it be unified with works-with::3Dmodel?
+
+Tag: works-with-format::abi		# Applied BIosystems. This one is not plaintext, I think.
+
+Tag: works-with-format::fitch        # neither this one
+
+Tag: works-with-format::biology:fasta
+
+Tag: works-with-format::biology:affy:dat
+Description: Scanner pixel-level raw data of Affymetrix microarray
+
+Tag: works-with-format::biology:affy:cel
+Description: Probe-level raw data of Affymetrix microarray
+  # I would rather move the above formats in the ::plaintext subfacet -- Charles
+  # This is fine with me. And what about affy:cdf? This could go to plaintext:cdf directly? -- Steffen
+
+Tag: works-with-format::plaintext:acedb
+
+Tag: works-with-format::plaintext:aln
+Description: Nucleotide or Protein sequence alignment
+
+Tag: works-with-format::plaintext:asn1
+Description: Abstract Syntax Notation 1
+
+Tag: works-with-format::plaintext:codata
+
+Tag: works-with-format::plaintext:dbid
+
+Tag: works-with-format::plaintext:embl
+Description: EMBL nucleotide sequence database format
+  This field should only be used for data that
+  is storing nucleotide data. Other historiacal
+  derivatives (PRINTS, UniProt, ...) should have
+  their own respective entry.
+
+Tag: works-with-format::plaintext:experiment
+
+Tag: works-with-format::plaintext:fasta
+
+Tag: works-with-format::plaintext:gcg
+
+Tag: works-with-format::plaintext:gff
+
+Tag: works-with-format::plaintext:hennig86
+
+Tag: works-with-format::plaintext:ij
+
+Tag: works-with-format::plaintext:intact
+Description: an interaction database -- Steffen
+
+Tag: works-with-format::plaintext:interpro
+Description: protein domain meta database -- Steffen
+
+Tag: works-with-format::plaintext:jackknifer
+
+Tag: works-with-format::plaintext:jackknifernon
+
+Tag: works-with-format::plaintext:mega
+
+Tag: works-with-format::plaintext:meganon
+
+Tag: works-with-format::plaintext:msf
+
+Tag: works-with-format::plaintext:nbrf
+
+Tag: works-with-format::plaintext:ncbi
+
+Tag: works-with-format::plaintext:nexus
+
+Tag: works-with-format::plaintext:nexusnon
+
+Tag: works-with-format::plaintext:paup
+
+Tag: works-with-format::plaintext:paupnon
+
+Tag: works-with-format::plaintext:pdb
+Description: Protein structure data
+
+Tag: works-with-format::plaintext:pfam
+
+Tag: works-with-format::plaintext:phylip
+
+Tag: works-with-format::plaintext:phylipnon
+Description: what is this? -- Steffen
+
+Tag: works-with-format::plaintext:pir
+
+Tag: works-with-format::plaintext:prints # protein domain/family database
+
+Tag: works-with-format::plaintext:raw
+Description: OK, that one advocates against the use of plaintext.
+
+Tag: works-with-format::plaintext:selex
+
+Tag: works-with-format::plaintext:staden
+
+Tag: works-with-format::plaintext:strider
+
+Tag: works-with-format::plaintext:stockholm
+
+Tag: works-with-format::plaintext:swissprot
+
+Tag: works-with-format::plaintext:treecon
+
+Tag: works-with-format::plaintext:affy:dat
+
+Tag: works-with-format::plaintext:affy:cel
+
+Tag: works-with-format::medicine:practice:xDT
+
+Tag: works-with-format::medicine:DICOM
+Description: or works-with-format::dicom ? -- Charles
+   I would like to prepare for  SNOMED, ICD10 and several others -- Steffen
+
 # an earlier idea of mine to separate different
 # kinds of prediction methods - appreciated?
 # "use" rather than "made-of"?
 # -- Steffen
-made-of::algorithm:dynamic-programming
-made-of::algorithm:hashing
-made-of::algorithm:hidden-markov-model
-made-of::algorithm:neural-network
-made-of::algorithm:dimension-reduction # to comprise ICA and PCA, spring-embedding -- Steffen
+Tag: made-of::algorithm:dynamic-programming
 
+Tag: made-of::algorithm:hashing
+
+Tag: made-of::algorithm:hidden-markov-model
+
+Tag: made-of::algorithm:neural-network
+
+Tag: made-of::algorithm:dimension-reduction
+Description: Comprises ICA and PCA, spring-embedding -- Steffen
+
 # some less arguable debtags:
-made-of::data:R # came up in my attempt to kind of homogenize biocViews with Debtags
+Tag: made-of::data:r # For the statistics environment http://www.r-project.org
 


