The Genex.pm Distribution
Welcome to Genex.pm, I hope you enjoy your visit.
Introduction
Genex.pm is a Perl module to enable bioinformatics researchers to
access a GeneX gene expression database (DB) via Perl. It provides an
application programmers interface (API) consisting of table classes and utility classes, and it also comes with a
tutorial and a number of example scripts to help researchers write their own
tools.
Table Classes
The majority of the modules included in the Genex.pm distribution
provide access to a single table in the Genex DB.
The purpose of the table classes is to
simplify accessing information from the DB by shielding many of the
DB's underlying details from the developer.
The table classes can be divided into three logical groups:
- Main data table classes
- AL_Spots.pm,
- AM_Group.pm,
- AM_Spots.pm,
- ArrayLayout.pm,
- ArrayMeasurement.pm,
- CanonicalSequenceFeature.pm,
- Chromosome.pm,
- Citation.pm,
- Contact.pm,
- ContactType.pm,
- ExperimentFactors.pm,
- ExperimentSet.pm,
- ExternalDatabase.pm,
- GroupSec.pm,
- Protocol.pm,
- Sample.pm,
- Scanner.pm,
- Software.pm,
- Species.pm,
- Spotter.pm,
- TreatmentLevel.pm,
- Treatment_AMs.pm,
- UserCanonicalLink.pm,
- UserSec.pm,
- UserSequenceFeature.pm,
- Linking table classes
- AM_FactorValues.pm,
- AM_SuspectSpots.pm,
- BlastHits.pm,
- CSF_ExternalDBLink.pm,
- CitationLink.pm,
- GroupLink.pm,
- HotSpots.pm,
- RelatedCSF.pm,
- SampleProtocols.pm,
- SpotLink.pm,
- TL_FactorValues.pm,
- USF_ExternalDBLink.pm,
- Controlled vocabulary table classes
- ALS_SpotType.pm,
- AL_Coating.pm,
- AL_DefaultSpotConcUnits.pm,
- AL_IdentifierCode.pm,
- AL_Medium.pm,
- AL_TechnologyType.pm,
- AM_EquationType.pm,
- AM_SpotMeasurementUnits.pm,
- AM_Type.pm,
- CSF_Type.pm,
- ControlledVocab.pm,
- EF_MajorCategory.pm,
- EF_MinorCategory.pm,
- ES_QuantitySeriesType.pm,
- ES_TreatmentType.pm,
- HS_ThresholdType.pm,
- PRT_Type.pm,
- SCN_ModelDescription.pm,
- SMP_AgeUnits.pm,
- SMP_DevelopmentStageName.pm,
- SMP_DevelopmentStageUnits.pm,
- SMP_GeneticStatus.pm,
- SMP_OrganType.pm,
- SMP_OrganismIntactness.pm,
- SMP_PrimaryCellType.pm,
- SMP_SexMatingType.pm,
- SMP_TissueType.pm,
- SPC_CellStructure.pm,
- SPC_GeneralClassification.pm,
- SPC_Generalclassification.pm,
- SPT_ModelDescription.pm,
- SPT_ModelName.pm,
- SW_Name.pm,
- SW_Type.pm,
- USF_Type.pm,
Utility Classes
Many of the mundane needs of developers working with a Genex DB have
been simplified by adding commonly used functions to helper
modules.
See the individual modules for more details:
- Genex.pm itself, which contains helper
functions for connecting to a GeneX DB, and
- DBUtils.pm, which contains helper
functions for retrieving and storing data in a GeneX DB, and
- HTMLUtils.pm, which contains
helper functions for converting information to HTML.
- XMLUtils.pm, which contains
helper functions for converting information to XML.
Author and Copyright
This module and its documentation were written by Jason E. Stewart
(jes@ncgr.org), and all the material
is copyright © 2000 the National
Center for Genome Resources.