Gus3.5RoadMap

• GUS 3.5 Has Been Released. This page is obsolete!*

Overview

GUS 3.5 is currently scheduled for release around the end of February/early March. From a feature perspective, GUS 3.5 primarly focuses on schema maintenance, official PostgreSQL support, and the introduction of Proteomics support. From an administrative perspective, GUS 3.5 represents a larger shift in how CBIL manages and releases GUS. This is reflected in a new administrative system providing schema maintenance functionality (included representing the official GUS schema as XML), enhanced installation support, and a RDBMS model for future functionality.

You may wish to browse the propsed GUS 3.5 schema (in progress) at http://www.gusdb.org/cgi-bin/schemaBrowser (The schema browser for GUS pre 3.5 is at http://www.gusdb.org/cgi-bin/schemaBrowserOld

GUS 3.5 Features and Fixes

Schema

• Lose the Core.Machine table and the link to it in AlgorithmInvocation

  • Migration

    • none

  • Applications

    • remove it from GusApplication.pm

• Core.ProjectInfo gains a 'release' column

  • Migration

    • none

  • Applications

    • none

• Changes to support database (not schema) level versioning. Drop VERSION from Core.DatabaseInfo. Create new table, Core.DatabaseVersion with one column to hold the version.

  • Migration

    • none?

  • Applications

    • Update GusApplication.pm

• Move MGED Ontology tables to a generic ontology. For now, this means renaming SRes.MGEDOntologyTerm to SRes.OntologyTerm and SRes.MGEDOntologyRelationship to SRes.OntologyRelationship

  • Migration

    • none *

  • Application code and plugins

    • Handled by the RAD team

• (schema) SRes.BibliographicReference will have three column changes. pubmed_id will become source_id, and medline_id will be removed, and external_database_release_id will be added.

  • Migration

    • set external_database_release_id to the pubmed entry for non-null source_ids.
    • (create pubmed in extdb)

  • Application code and plugins

    • misc/bibliographicReference.php
    • misc/bibliographicReferenceUpdate.php
    • RAD/php/misc/bibliographicReference.php
    • RAD/php/misc/bibliographicReferenceUpdate.php
    • RAD/StudyAnnotator/misc/bibliographicReference.php
    • RAD/StudyAnnotator/misc/bibliographicReferenceUpdate.php
    • RAD/MR_T/lib/perl/MageExport/Description.pm
    • RAD/MR_T/lib/perl/MageExport/Experiment.pm

• DoTS.GeneAlias will be removed.

  • Migration

    • move the rows into DoTS.GeneSynonym

  • Application code and plugins

    • none so far

• DoTS.NASequenceImp and DoTS.AASequenceImp will have sequence_ontology_id columns added. Their sequence_type, and sequence_ontology_id fields will be nullable.

  • Migration

    • none

  • Application code and plugins

    • InsertNewExternalSequence
    • RAD/MR_T/lib/perl/MageExport/BioSequence.pm
    • RAD/Querier/htdocs/SResDownload.txt
    • GUS/Common/lib/perl/Bioperl2Gus.pm
    • GUS/Common/plugin/perl/GBParser.pm
    • GUS/Common/plugin/perl/InsertNewExternalSequences.pm
    • GUS/Common/plugin/perl/dbEST.pm
    • GUS/Common/plugin/perl/LoadGeneFeaturesFromXML.pm
    • GUS/Common/plugin/perl/GenericParser2Gus.pm
    • GUS/Common/plugin/perl/TruncateTables.pm
    • GUS/Website/htdocs/documentation/installguide_UGA.html
    • PlasmoDB/Loader/plugin/perl/LoadGeneFeaturesFromXML.pm

.

• DoTS.GeneInstance, DoTS.RNAInstance, and DoTS.ProteinInstance will have the fields to the *InstanceCategory tables nullable.

  • Migration

    • none

  • Application code and plugins

    • none

• DoTS.Gene, DoTS.RNA, DoTS.Protein columns for category will become nullable. The tables will gain a sequence_ontology_id column.

  • Migration

    • none

  • Application code and plugins

    • none

• All foreign keys to ReviewStatus will be nullable. A null value is interpreted as not reviewed.

  • Tables effected

    • DoTS::AllelePhenotypeClass DoTS::AlleleInstance TESS::ActivityImp DoTS::AASequenceEnzymeClass DoTS::Complementation DoTS::ComplexAnatomy DoTS::GeneInstance DoTS::Protein SRes::ExternalDatabaseEntry DoTS::GOAssociationInstance TESS::ParameterGroup DoTS::AAMotifGOTermRuleSet DoTS::GOAssocInstEvidCode DoTS::RNAInstance DoTS::GOAssociation DoTS::RNAIConstruct DoTS::Gene DoTS::AAMotifGOTermRule DoTS::RNA TESS::MoietyImp TESS::ModelResult DoTS::ProteinSynonym DoTS::GeneSynonym TESS::ModelImp TESS::PredictionResult DoTS::AlleleComplementation DoTS::Comments DoTS::ProteinInstance TESS::MoietyMember TESS::Analysis DoTS::Complex DoTS::Interaction DoTS::RNAIPhenotype DoTS::AllelePhenotype

  • Migration

    • none
  • Applications ?

• (schema) a new global analysis table ( Core.AnalysisAlgorithm) will be introduced, allowing any given row to have information about a particular analysis algorithm, in addition to the row_algorithm_id, which usually just contains information about the plugin loading the data. As part of this change, algorithm_id will be removed from DoTS.Similarity, DoTS.SeqGroupExperimentImp (and views), and DoTS.OpticalMapAlignment.

  • Migration

    • Similarity

      • none: algorithm_id is null in all rows (cbilbld)

    • SeqGroupExperiment

      • none? (tables not yet used...)

    • OpticalMapAlignment

      • is it really worth it?

  • Application code and plugins

    • Similarity

      • none - no plugin fills this value

    • SeqGroupExperiment

      • none? (tables not yet used...)

    • OpticalMapAlignment

      • none? (no plugin found for this)
• A new TransmembraneAAFeature view will be introduced:

create view dots.TransMembraneAAFeature as
select  aa_feature_id,
aa_sequence_id,
feature_name_id,
parent_id,
na_feature_id,
subclass_view,
sequence_ontology_id,
description,
pfam_entry_id,
motif_aa_sequence_id,
repeat_type_id,
external_database_release_id,
source_id,
prediction_algorithm_id,
is_predicted,
review_status_id,
int1 as length,
string1 as expected_aa,
string2 as first_60,
int2 as predicted_helices,
int3 as topology,
MODIFICATION_DATE,
USER_READ,
USER_WRITE,
GROUP_READ,
GROUP_WRITE,
OTHER_READ,
OTHER_WRITE,
ROW_USER_ID,
ROW_GROUP_ID,
ROW_PROJECT_ID,
ROW_ALG_INVOCATION_ID
from DoTS.AaFeatureImp where subclass_view='TransMembraneAAFeature';

• Migration

  • none

• Application code and plugins

  • none

• All subclasses will be reviewed to make sure they have all attributes of the superclass.

  • Migration

    • none
  • Application code and plugins

• Dots.AASequenceImp will have a taxon_id column added.

  • Migration

    • none

  • Application code and plugins

    • LoadNRDB?

• DoTS.AASequenceImp.Description will increase to be a Varchar2(2000)

  • Migration

    • none

  • Application code and plugins

    • not affected

• DoTS.PlasmoMap will have the cross columned renamed to outcross due to a Postgres conflict.

  • Migration

    • none
  • Application code and plugins

• Tess.RegionOfInterest, Tess.PredictedBindingSite, Tess.IslandOfInterest will have the end column renamed to end_position and the begin column renamed to begin_position due to a Postgres conflict.

  • Migration

    • none
  • Application code and plugins

• SRes.Reference (and version table) has three columns increasing to a VARCHAR2(1000): journal_or_book_name, author, and title

  • Migration

    • none

  • Application code and plugins

    • not affected

• DoTS.Library (and version table) has several columns whose length are increasing-- all to VARCHAR2(156): Vector, Tissue_Type, Strain, Cultivar, Cell_Type

  • Migration

    • none

  • Application code and plugins

    • not affected

• SRes.ExternalDatabase will have the lowercase_name column removed.

  • Migration

    • none
  • Application code and plugins

RAD

• The RAD3 schema will be renamed to RAD

• Introduction of Proteomics support. A new PROT schema space will initially support mass spectrometry results, and will eventually be extended to 2D-Gel and other separation techniques. A new STUDY schema space will compile information general to high-throughput experiments, such as microarray and proteomics. Encompasses Protocols, Study Designs, and BioMaterial Preparation. As part of this change, all RAD3 study tables will move to the new STUDY schema. This includes RAD3.BioMaterialCharateristic, RAD3.BioMaterialImp, RAD3.BioMaterialMeasurement, RAD3.Study, RAD3.StudyDesign, RAD3.StudyDesignDescription, RAD3.StudyDesignType, RAD3.StudyFactor and associated views (RAD3.BioMaterial, RAD3.BioSample, RAD3.LabeledExtract, RAD3.BioSource). RAD3.Channel will remain in RAD3 (and not be in STUDY)

  • Migration
  • Application code and plugins

• RAD3.Array will get a new nullable field, surface_type_id (number 10), which will be a foreign key to RAD3.OntologyEntry.

  • Migration

    • none
  • Application code and plugins

• RAD3.CompositeElementImp, RAD3.Array, RAD3.Protocol, and RAD3.Study have all had their External_DB_Release_ID fields increased to number(12).

  • Migration

    • none
  • Application code and plugins

• RAD3.ElementImp will have two new nullable fields, physical_biosequence_type_id, polymer_type_id (both NUMBER(10), and both will have foreign keys to RAD3.OntologyEntry).

  • Migration

    • none
  • Application code and plugins

• RAD3.AcquisitionParam, RAD3.QuantificationParam, RAD3.AnalysisParam, and RAD3.AnalysisQCParam (and all associated version tables) will have the value column increased to a varchar2(100).

  • Migration

    • none

  • Application code and plugins

    • not affected

• RAD3.Array will be renamed to ReporterArray due to a Postgres conflict.

  • Migration

    • none
  • Application code and plugins

• RAD3.ScanAlyzeElementResult will have the left column renamed to left_coordinate, right column renamed to right_coordinate, top column renamed to top_coordinate, and bottom column renamed to bottom_coordinate due to a Postgres conflit. This is a view.

  • Migration

    • none
  • Application code and plugins

• RAD3.ProcessImplementation, RAD3.ProcessImplementationParam, RAD3.ProcessInvocation, RAD3.ProcessInvocationParam, RAD3.ProcessInvQuantification, RAD3.ProcessIO, and RAD3.ProcessResult have been deprecated.

  • Migration

    • No migration scripts will be provided.
  • Application code and plugins

• RAD3.Analysis will have analysis_date updated to be nullable.

  • Migration

    • None

  • Application code and plugins

    • None

• RAD3.GNFAffymetixResult has been deprecated

  • Migration

    • None (view)
  • Application code and plugins

Object Layer

• Issue with nulls in numeric data types for Postgres (this needs review).
• GBParser: Use of IMP Table, Use of sysdate (this needs review).

Administrative & Miscellaneous

• Improved Installation System, including a single configuration file, automatic schema and metadata installation into Oracle or Postgres, and a pipeline for loading initial data.
• PostgreSQL Support
• New, complete documentation