Diff for "RFC_1/RFC1_Comment_Attribute_Names"

EthanCerami, 10/1/2005 - While we are at it, perhaps we should consider creating a class called CyAttributeNames, that will contain a list of recommended / officially supported attribute names. This would be similar to a controlled vocabulary list, but would not actually be enforced by CyAttributes. For example, CyAttributeNames will include constants for attributes, such as COMMON_NAME, CANONICAL_NAME, SPECIES, COMMENT, DATABASE_SOURCE, SEQUENCE, etc. If we all use these recommended terms, it's a bit easier to share data between plugins, and we can also create more meaningful attribute browsers. We can then modify the javadocs for each of the setters in CyAttributes to say something like: 'You are free to use any attribute name you like. However, for maximal benefit, consider using one of the recommended attribute names in CyAttributeNames.' I think we have talked about doing this for a real long time, and now is probably the time to do it.

Here is a proposed first draft of CyAttributeNames

   1 package cytoscape.data;
   2 
   3 /**
   4 * Comments go here...
   5 **/
   6 public class CyAttributeNames {
   7     public static final String CANONICAL_NAME = "canonicalName";
   8     public static final String COMMON_NAME = "commonName";
   9     public static final String ORGANISM_SPECIES_NAME = "organism_species";
  10     public static final String ORGANISM_COMMON_NAME = "organism_common_name";
  11     public static final String ORGANISM_NCBI_TAXONOMY_ID =
  12             "organism_ncbi_taxonomy_id";
  13     public static final String SEQUENCE = "sequence";
  14     public static final String MOLECULE_TYPE = "molecule_type";
  15     public static final String GO_MOLECULAR_FUNCTION = "molecular_function";
  16     public static final String GO_BIOLOGICAL_PROCESS = "biological_process";
  17     public static final String GO_CELLULAR_COMPONENT = "cellular_component";
  18     public static final String COMMENT = "comment";
  19     public static final String DESCRIPTION = "description";
  20     public static final String PUB_MED_ID = "pub_med_id";
  21 }
  22 

IlianaAvila - 10/3/05 - We have cytoscape.data.Semantics, which contains static names like CANONICAL_NAME, COMMON_NAME, INTERACTION, etc. Would we deprecate it?

GaryBader - 10/4/05 - I think most of these semantics should be moved into semantic plugin packages so that people can swap in the PSI-MI semantics for the BioPAX semantics for the xyz semantics, etc. We would need to better organize these attribute names to avoid generating a huge flat list in CyAttributeNames. Maybe some basic attribute names should be available. As Iliana mentioned, these are in data.Semantics - we should re-evaluate that class to see if it's accessible enough for users.