[MOBY-l] Service Hierarchy Attempt

Fri May 3 15:51:57 UTC 2002

On 1 May 2002, Jason E. Stewart wrote:

> Hey All,
> 
> Here's the start of the ServiceType Ontology. It would be nice if
> someone with DAG-Edit knowledge could make this a little nicer, and
> maybe we could toss up an HTML version of it on the moby site using
> Amigo.
> 
> jas.
> --

Hi,

OK, I've put this through DAG-Edit, generating 'STO' IDs. I made a few
small changes, mostly correcting typos or case but I also made some of the
terms more verbose (e.g. alignment -> sequence alignment). I made a stab
at a few rudimentary definitions; I would not mind in the least if anyone
feels motivated to modify or even scrap them. If no one else wants to do
it, I can continue doing a bit of digging to come up with defintions for
everything (eventually).

I've attached two files, servicetype.ontology and servicetype.defs, in GO 
flat file syntax as output by DAG-Edit.

I also have a few questions:

 - Does anyone remember why BLAST and Smith-Waterman went under functional
assignment (which I changed to function prediction)? Smith-Wateramn
is a sequence alignment algorithm, and BLAST finds similar sequences given
an input sequence, so I moved both. (We can make the STO a DAG if they
should be under functional whatever after all.)

 ... which leads to another question:
 - Should BLAST also be an instance of sequence alignment?

 - Should alignment go under sequence comparison (formerly sequence
similarity)?

 - What do we mean by 'phylogenetic' service? I wanted to make this one
more verbose but didn't know what we wanted to say. 'Phylogenetic
comparison'? 'Phylogenetic analysis'?

 - Do we want to include input and output MOBY objects or object classes
in the definitions?

Sorry to dwell on the details so much; its just that this is one area
where I can make a meaningful contribution to MOBY!

Cheers,
Midori

-------------- next part --------------
!autogenerated-by:     DAG-Edit version 1.311
!saved-by:             midori
!date:                 Fri May 03 16:48:19 BST 2002
!version: $Revision: 1.6 $
$Service_Type_Ontology ; STO:0001
 %Computational service ; STO:0002
  %Clustering ; STO:0019
   %Hierarchical clustering ; STO:0020
   %Non-hierarchical clustering ; STO:0021
    %K-Means clustering ; STO:0022
    %Self-organized maps ; STO:0023
  %Function prediction ; STO:0028
  %Gene prediction ; STO:0005 ; synonym:gene finding
   %Eukaryotic gene prediction ; STO:0008 ; synonym:eukaryotic gene finding
    %Genscan ; STO:0009
    %Grail ; STO:0010
   %Prokaryotic gene prediction ; STO:0006 ; synonym:prokaryotic gene finding
    %Glimmer ; STO:0007
  %Hydrophobicity ; STO:0016
  %Pattern finding ; STO:0013
   %Restriction mapping ; STO:0014
   %Transcription factor binding site prediction ; STO:0015
  %Phylogenetic ; STO:0004
  %Primer discovery ; STO:0033
  %Repeat finding ; STO:0017
  %Repeat masking ; STO:0018
  %Sequence alignment ; STO:0024
   %Multiple sequence alignment ; STO:0026
   %Pairwise sequence alignment ; STO:0025
    %Smith-Waterman ; STO:0029
  %Sequence assembly ; STO:0003
  %Sequence comparison ; STO:0027
   %BLAST ; STO:0030
    %NCBI-BLAST ; STO:0031
    %WU-BLAST ; STO:0032
  %Structure prediction ; GO:0030001
   %Protein structure prediction ; GO:0030002
   %RNA secondary structure prediction ; STO:0011
  %Translation service ; STO:0012
 %Retrieval service ; STO:0034
 %Submission service ; STO:0035
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!version: $Revision: 1.6 $
!date:                 Fri May 03 16:48:19 BST 2002
!saved-by: midori
!autogenerated-by: DAG-Edit version 1.311
!
!Gene Ontology definitions
!
term: Computational service
goid: STO:0002
definition: Any service that performs a computational analysis based upon the input.
definition_reference: MOBY:mah

term: Function prediction
goid: STO:0028
definition: Predicts a function or functions for an input amino acid sequence. Output is a set of GO IDs corresponding to predicted functions.
definition_reference: MOBY:mah

term: Multiple sequence alignment
goid: STO:0026
definition: Determines the optimal alignment between sets of more than two input sequences of nucleic acid or amino acid residues.
definition_reference: MOBY:mah

term: Pairwise sequence alignment
goid: STO:0025
definition: Determines the optimal alignment between two input sequences of nucleic acid or amino acid residues.
definition_reference: MOBY:mah

term: Protein structure prediction
goid: GO:0030002
definition: Predicts structural features of all or part of a protein.
definition_reference: MOBY:mah

term: Retrieval service
goid: STO:0034
definition: Any service that retrieves data from a database or other data source.
definition_reference: MOBY:mah

term: RNA secondary structure prediction
goid: STO:0011
definition: Predicts secondary structural features of all or part of an RNA molecule.
definition_reference: MOBY:mah

term: Sequence alignment
goid: STO:0024
definition: Determines the optimal alignment between sets of input nucleic acid or amino acid sequences.
definition_reference: MOBY:mah

term: Smith-Waterman
goid: STO:0029
definition: An algorithm for performing local alignments of two sequences.
definition_reference: MOBY:mah

term: Submission service
goid: STO:0035
definition: Any service that doesn't return a MOBY object.
definition_reference: MOBY:jas

term: Translation service
goid: STO:0012
definition: Converts an input nucleotide sequence into predicted amino acid sequence.
definition_reference: MOBY:mah