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September 2003 GMOD Meeting
Generic Model Organism Database Construction Set
September 15-16, 2003
The third GMOD working group meeting was held at Lawrence Berkeley National Laboratory on September 15th and 16th. Below are the presentations given by the groups represented, and below that is the text of progress reports they submitted.
PubSearch Status Update
PubSearch status as 0f 9/05/2003)
Upgrades made to the PubSearch software are as follows:
- Search Interface Cleanup For:
- Cleanup & Finalization of Installation Scripts
- GUI Interface -- migrated to Java Swing
- Validating DB connection between PubSearch (Java Servlets) & DB.
- Automatic Installation of Schema into DB (code re-organization required -- In Progress)
- Auxiliary PubSearch DataFiles
- Includes Indexing Directories
- Cached DTD's (from GeneOntology & PubMed)
- Testing (To Be Performed)
- Generic Schema (generic_pub)
- Completed (includes: data associated with the Pub database, Table name adjustments, Field name adjustments, Data Type Adjustments). This effort does not include `update_history' table (in progress).
- Installed MySQL 4.0 (to address referential Integrity)
- Development of Data parsers for Bulk Loading
- Articles (Using Medline Format)
- Schema Documentation
- Completed the 1st version (addresses `pub database', documentation for `generic_pub' is yet to be completed)
- Software Documentation
- In progress
Pathway Tools Status Report
Pathway Tools status report, by Peter Karp, September 1, 2003
Please note that the full history of updates to Pathway Tools can be found at URL
Significant updates funded under this grant since the last report are as follows.
- A new release of Pathway Tools occurred on August 29, 2003.
- A general import/export facility for frames (DB objects) has been added. Sets of frames can be exported to and imported from character-delimited files, which can be imported into a spreadsheet program, edited, and re-imported. Frames can also be exported to an attribute-value format similar to MEDLINE format, and re-imported into a different DB.
- An ontology of evidence codes has been added to the Pathway Tools schema, in order to capture the evidence (computational, experimental, type of experiment, etc.) for the existence of various entities (pathways, protein functions, transcription units, etc.) in an organism. Pathway Tools has been extended so that the pathway and operon predictors within PathoLogic decorate the pathway and operon PGDB objects that they create with evidence-code information, indicating computationally predicted objects as such. The Editors have been extended to include functionality that allows users to interactively enter and modify evidence codes within PGDB objects. The Navigator has also been extended to display evidence information.
- Changes to the Pathway/Genome Navigator
- Desktop mode (not Web mode): Several new types of queries have been added:
- Query pathways by reactants and products.
- Query proteins by molecular weight and pI.
- Query compounds by conjunctions of name, molecular weight, chemical formula, and substructure properties.
- Desktop mode (not Web mode): Several new types of queries have been added:
- Displays of the parent classes of an instance have been reworked to be more intuitive; they now show the complete class inheritance path back to the roots of the class hierarchy.
- It is now possible to install Pathway Tools with any of the buttons on the main query page (help, pathway tools home, etc.) redirected to a custom user-specified URL.
- The list of reactions in the compound display is sorted according to the role that the compound plays in each reaction.
- Changes to the Pathway/Genome Editors
- There is now an editor for RNAs, which also allows the creation of RNAs for genes.
- The compound structure editor now allows charges to be entered along with each atom.
- 37 groups have licensed Pathway Tools to date.
- Pathway/Genome Databases available through the web include:
Chado progress report * Schema development (Colin Wiel, Chris Mungall, David Emmert, Stan Letovsky) * The first production version, tagged �chado_1_01�, released in July, 2003. * This version is sufficient for managing genome sequence and annotation data. The sequence, cv, dbxref, and companalysis modules are effectively finished. * Plans for FlyBase genetic module review * FlyBase developers will meet for four days at the end of October to review the genetic and map modules preliminary to integrating FlyBase genetic/phenotypic data with genome sequence and annotation already in chado. * Current development of expression module * Allen Day has been working on the expression module in his own branch of chado. * Current development of pub module * Peili Zhang has been working on migrating FlyBase publications data into the pub module * ChadoXML DTD and related tools (Pinglei Zhou, Stan Letovsky) * DTD for ChadoXML and tools which convert database ddl into DTD are released on GMOD. * XORT- XML Object to Relational Translator (Pinglei Zhou, Stan Letovsky) * XORT exchanges data between XML file and database. XORT is generic enough to handle any relational database as long as schema follows certain fairly broad design rules. * It includes validator, loader, dumper and XORTDiff. Dumper is driven by dump spec to meet different projects� requirements. XORTDiff, which is schema-aware, can compare ChadoXML objects and is very useful in testing. * GAME2ChadoXML/ChadoXML2GAME translator (Frank Smutniak, Stan Letovsky) * Final debugging is in process as we use this software in the creation of D. melanogaster release 3.2. * Round-tripping of annotation data is essentially finished * Round-tripping of computational analysis data will need additional debugging * GenBank flat-file format to chadoXML converter (Peili Zhang, Chris Mungall) * A bioperl module, chadoxml.pm, is being developed to convert sequence and annotation data from whole genome projects deposited in GenBank into chadoXML. * The module makes use of the Unflattener.pm bioperl module by Chris Mungall, which generates chado gene models out of properly formatted GenBank gene model features (gene, mRNA and CDS). * The converter is working well for D.melanogaster data, and work is in progress to make it able to handle other genome data sets. Textpresso: A progress report Eimear Kenny, Hans-Michael Mueller and Paul Sternberg In April, 2003, we reported our progress on Textpresso, an information retrieval and extraction system for C. elegans literature. The Textpresso system is based on shallow text parsing to identify terms of interest, which have been organized into ontologies, in a corpus of ASCII journal abstract and article text. The parsed text is outputted as XML and search-able by either keywords and/or ontology categories via a user-friendly interfaces (www.textpresso.org). This tool is being generated for use at both a general user-level and a curator-level, and ultimately, for automatic extraction of biological facts from text. We would like to report the following progress since April: Installed Textpresso on a new Server Textpresso has a new home on a 2.8 GHz Pentium Xeon dual processor, 3GB RAM, 280GB SCSI HD server! Added Endnote export functionality Citation information for returned abstracts can now be exported in Endnote format (with or without including the abstract) Added 700 full text articles The full text of ~700 journal articles from the CGC bibliography (primarily from the last two years) have been added to the Textpresso corpus. This is the result of the implementation of a novel software for converting PDF to text (see below). We plan to add another ~900 C. elegans information-rich articles from PubMed by mid-October. Imminent release of pdf2text software for Journal articles We have developed and implemented on novel software, written by Robert Li at Caltech, for converting biological journal articles in PDF format to correctly flowing ASCII text. The software is written in python and relies on journal specific templates. We plan to release this software on sourceforge very soon, including a library of ~100 Journal templates (generated by Daniel Wang at Caltech) and full documentation on how to construct new templates. Textpresso paper ... in progress We are busy writing and hope to publish in the coming months. First foray into Fact Extraction using Textpresso We have automatically extracted ~14,000 unique locus<->allele<->reference relationships from the full text of ~2000 C. elegans journal articles. Mouse Genome Informatics In our grant supplement, we proposed four specific projects to contribute to the GMOD software libraries: a tool for building and maintaining customized sets of blastable sequence databases; a laboratory notebook for capturing expression data, with facilities for electronic data submission; a web-based browser interface designed for exploring structured vocabularies (ontologies); and a tool for displaying summarized orthology data against a reference genome background. These projects were selected from the many already underway or planned at MGI at the time of the application. Our overall plan is to develop and use the tools first in the context of the MGI project and then to package them for release to external groups. In the past year, we have made significant progress toward our goals. SeqDB Engine is a tool to support the construction and maintenance of customized sets of blastable databases. It allows us to deal with multiple sources of sequence data; differing release schedules and formats; the need to "filter" the incoming sequences according to organism and/or sequence type; the need to "route" sequences to one or more output databases; the need to manage large numbers of intermediate result files; and the need to deal efficiently with very large data sizes. Seqdb_engine is used at MGI to build the databases served by MouseBLAST (http://mouseblast.informatics.jax.org). This includes 18 separate blastable databases derived from 6 different data providers. SeqDB Engine is also used to maintain an even larger set of databases for MGI curatorial use. During the past several months, seqdb_engine has been modified to handle GenBank incremental updates. As well, because seqdb_engine depends on several other MGI components, we have developed an automated process for rebundling seqdb_engine for external distribution. Seqdb_engine has been submitted to the GMOD web site. The Gene Expression Notebook (GEN) is an Excel spreadsheet designed to be a laboratory notebook for recording gene expression data. It was designed to meet the needs of small to medium size labs performing the traditional expression assays (blot assays and in situs). It provides a large number of controlled vocabularies and provides a structured, standardized way to describe assays, reagents, and specific results. GEN supports images as well as text and numeric data. GEN also provides facilities for electronic data submission, currently to the GXD Database. GEN is currently available from the GMOD site. During the past several months, we have been porting GEN to Windows 2000 and to Mac OS/X. (Despite being an Excel application, differences in Excel across platforms and versions cause GEN not to run reliably in all cases.) W2000 and OS/X versions of GEN will be released as soon as they are validated. In the GMOD grant supplement, we proposed contributing MGI's ontology browser software, which provides a HTML-based interface for exploring the GO ontologies and other vocabularies. Developments in the intervening months warrant a change in direction. We have recently developed a prototype graphical viewer based on the GraphViz package from AT&T. This viewer is similar to, but developed independently from, SGD's GO Term Finder. It is written in Python and comprises several general, reusable software components, including libraries for general directed graphs, customizable graph traversals, and creating graph visualizations via GraphViz. We will soon submit the core libraries to GMOD, and follow up with the viewer application itself after another round of refinement. The Orthology Map Viewer was originally developed for MGD as a way to display a global overview of the mouse/human and mouse/rat orthology data. Rather than display conserved segments (which requires deciding where the boundaries are), we show histograms indicating the number of data points (i.e., orthologies) at the corresponding mouse genetic location. Multiple histograms are displayed along each mouse chromosome, corresponding to the orthologs' chromosomes. There is no progress on the viewer to report at this time. Apollo progress: Since May 2003, we have fixed various bugs and added some new functionality to Apollo, including: - Apollo now has an alignment viewer (an adapted version of Jalview) that lets you view DNA and/or protein features aligned with a three-frame genomic translation. - BOP has been merged into Apollo so you can now load and filter raw analysis results directly into Apollo. Current analysis types supported are BLAST, sim4, Genscan, and FgenesH. You can load the analysis results into a fresh Apollo session or layer them on top of the currently displayed region. - More support for non-gene annotations. - The GFF adapter now lets you specify a FASTA sequence file to load along with the GFF file (either in the GUI or from the command line). - Ported Apollo to JDK1.4 and fixed all the issues caused by the switch. - Window around requested genes now configurable. - Find by name now adds implicit final wildcard (full regular expression support coming soon). - More debugging of annotation info window. Also, you can now have multiple annotation info windows open at once. - Did a lot of testing and validation of XML saving, to make sure curators using Apollo don't lose any information and that the XML survives a round trip through Chado. We are currently discussing specifications for an improved synteny viewer that will let users look at detailed cross-genome comparisons and use them to refine and edit annotations, and also to look at comparisons between multiple genomes rather than just two. BOP progress: BOP has been merged into the Apollo codebase, so you can now run BOP either standalone from the command line or interactively from within Apollo. The Apollo interface currently supports parsing and filtering of results from BLAST, sim4, Genscan, and FgenesH. GUIs let the user control the filtering parameters. Additional parsers are in progress. BOP can now generate cigar strings to represent gapped alignments in a compact format. This allows the alignments to be viewed in Apollo's alignment viewer. GBrowse Contact: Lincoln Stein, email@example.com During the period from May to September 2003 we did not add many new features to GBrowse, but have worked steadily to improve its documentation and the install experience. All the documentation for GBrowse has now been put into Perl .pod format, and it is now automatically converted into HTML and installed on the user's web site. The installation procedure also creates a sample in-memory database (yeast chromosome 1), so that the new user can begin interacting with the browser immediately after installing it. There are new import filters for GenBank, EMBL and UCSC data files. This means that one can new initialize GBrowse databases using flat files in one of these formats. There is also support for the proposed GFF3 format. Plugins for FGENESH and GENSCAN have now been released. These plugins allow de novo gene predictions to be applied to genomes while the user is browsing. In terms of data sets, Nathan Siemers and Donald Jackson of Bristoll Myers Squibb has graciously donated a GBrowse-compatible file of TBLATSX annnotations comparing fly, mouse, human worm and zebrafish. These annotations are available for download on the Sourceforge web site, along with their tool for converting blast hit files into compatible GFF files. Xiaokang Pan of Iowa State has donated a GFF load file for Arabidopsis. We still are missing load files for mouse and human, and seek volunteers to generate these data sets. At the back end, Chado support seems pretty solid, and a variety of index optimizations now make the experience of browsing a fully populated Chado database nearly as good as browsing the simple Bio::DB::GFF databases. Bio::DB::GFF, meanwhile, has been enhanced to support live updates and deletes. This has made it possible to write plugins for GBrowse that allow for interactive updating of the database. In other news, Nat Goodman's group at Integrated Systems Biology has released "ISB GBrowse," a version of GBrowse that has been modified to use multiple datasources, including DAS sources. Because ISB GBrowse involves changes both to GBrowse and to Bioperl, it will take some time to bring these desirable modifications into the main GBrowse branch. Mark Wilkinson and Sheldon McKay, under a CSHL-administered USDA contract, have created a GBrowse-based genome curation system for use at the Meat Animal Research Center (MARC) in Nebraska. The system allows MARC scientists to maintain annotations across a large number of variant foot & mouth disease and chicken influenza virus genomes. The front end uses the Sanger Center's Artemis as the editor, and communicates with an Oracle-based Bio::DB::GFF database at the back end via a GBrowse plugin. The initial plan was quite different: to use Ensembl as the backend and Apollo as the front end. At the meeting, Sheldon McKay will discuss the evolution of the MARC project, a story that will illustrate the difficulties we face in taking GMOD from a collection of useful tools to a working integrated architecture. PubFetch/PubTrack Progress Report (September 2003) PubFetch Created initial public PubFetch webservice using BioMOBY protocol to provide access to PubMed literature database. The service can be tested at http://prometheus.brc.mcw.edu/pubfetch-bin/MOBY-Client05.cgi and is also available via MOBY Central: http://mobycentral.cbr.nrc.ca/cgi-bin/Client/MOBY-Client05.cgi and as a MOBY service available via MOBY Central for MOBY clients. Two services are currently available: the first runs a keyword search at PubMed and returns the PubMed Ids of matching articles, the second uses a PubMed ID and returns the PubMed record in MEDLINE format. The PubMed service uses Perl and existing RGD code with a MOBY wrapper. A second prototype service has been developed to access the Agricola literature database in a similar fashion. Unfortunately Agricola provides a web/CGI interface to its literature data requiring a somewhat crude approach to running searchers and retrieving results from the database. This service is not yet available as a public MOBY service. The Agricola service was developed as a java application with a MOBY wrapper. Our next step is to connect the PubFetch service with PubSearch via BioMOBY to enable PubSearch to use PubFetch as its literature data source. Implementation of PubSearch at RGD We have been working with the TAIR developers to install and populate at PubSearch database at RGD. This process has turned up a variety of dependencies that existed in the TAIR software that we have been working to remove to create a generic PubSearch database and tool. Currently RGD genes and curated literature has been loaded to PubSearch along with the GO terms. Based on these experiences a more robust loading script is being developed by TAIR that will greatly simplify data loading for new users of the tool. Automatic hit generation between articles and GO terms is fully functioning, we are working with TAIR to resolve some issues related to Gene-Article hit generation. Once the features of PubSearch are fully functioning we will begin to test the tool as part of the general RGD curation process. It is anticipated this will lead to a variety of suggested modifications that will further the flexibility of the PubSearch tool for use by other MODs. PubTrack We have continued to collect use cases for PubTrack and discuss the utility for TAIR and RGD use of PubSearch. Review of similar projects has lead us to discover a wide variety of related software (both within GMOD � BioPipe, GUS Workflow, and in the commercial arena) that we are now evaluating to see if they can be used as is or to learn more about alternative approaches to this problem of tracking information (data) within an organization (MOD). It is anticipated that significant progress will be made towards an initial prototype for PubTrack in the next quarter. GMOD project update, Sept 2003, Don Gilbert ------------------------------------------ Project goals ------------- Two proposed and one unproposed projects are in development as generic model organism database components for GMOD: A Genome Information Search and Retrieval module (GISR) of flexible data and text search software is an efficient and responsive tool for high-volume genome data of diverse source and content. A Data Grid Distribution module (DGD) uses emerging Science Grid technology to let organism databases provide computable directories and access to their high volumes of data. Additionally, A Replicable Genome infOrmation System (ARGOS) is being developed in conjunction with FlyBase project needs, to evolve the current FlyBase distributable server system into a generic framework for organism databases. Recent progress --------------- ARGOS A Replicable Genome infOrmation System ~~~~~ Argos provides automated replication for a framework genome data system, including common genome tools and Internet information services, with flexible project web look and functions, data mining methods. This is nearing production use for building and distributing genome db systems, including for FlyBase and euGenes genome systems. It has a new Daphnia organism genome project, and a sample organism project (CentaurBase) for testing. Recent functional updates include common Perl (including BioPerl, XML tools and others) and Java libraries; load balancing for a cluster of replicated servers; fuller integration of NCBI BLAST; addition of a secure WebDav web-editing interface; addition of LuceGene for XML, biosequence and data searching; Axis for web services and JavaLDAP for data access (in test mode). The reference service is at http://flybase.net/flybase-ng or http://eugenes.org/argos with project documentation at http://www.gmod.org/argos The Daphnia Genome Consortium will have a full genome sequence in the coming 6 months, funded by DOE-JGI and various NSF and EPA projects. I've been advising them on genome databases, leaning toward using GMOD and related genome tools, including GBrowse, CMap, Apollo, with some dithering between choices of Chado-Postgres or EnsEMBL for a data management system. We have fashioned a proto-Daphnia database (wFleaBase) based on Argos, at http://iubio.bio.indiana.edu/daphnia with details in its documents section. Developments in this include tests of LuceGene, WebDav access for secure editing of project documents, and other parts which are being folded into GMOD source distributions. GISR Genome Information Search and Retrieval module ~~~~ Originally proposed to use the well-known SRS bioinformatics data system, we now are focusing on Lucene open-source text indexing tool for this GMOD project. Both SRS and Lucene provide for efficient search/retrieval of high-volume, semi-structured and complexly structured data that doesn't always fit easily a relational database structure, allowing organism/genome databases to more easily offer access to a wider range of information at lower personnel costs. We recently developed this into LuceGene (pronounced as 'Lucy Jean') using Lucene (jakarta.apache.org/lucene). Initial testing has proven its recognized abilities as an efficient, high-volume IR program. It is capable at handling gigabyte data sets of millions of objects, at levels similar to the SRS system. It can, with appropriate data parsing adaptors, index and search all fields of objects, and includes a common set text search features (booleans, phrases, fuzzy searches, word stemming, field range searches) common in Google and related Internet web search systems. LuceGene additions to Lucene include adaptors for parsing FlyBase data, XML (including Medline XML), GenBank and related biosequence data. Test cases include all of data in FlyBase.net and euGenes.org projects, samples from Medline, GenBank, and others. Performance has been good, but further development will be needed before it can be used as a replacement for current FlyBase functions. The original proposal for this GMOD project was to use SRS, as now used in FlyBase. This software is copyrighted by Thure Etzold and colleagues (originally developed at EMBL/EBI) and newer versions are owned by Lion Biosciences, who provide for free academic uses. Though we had initial agreements to use SRS w/in the GMOD project, over the past year Lion Biosciences has become more restrictive in its academic licensing of SRS, and our current agreement is to remove SRS in its current version from FlyBase, and not include it in GMOD project as envisioned. For a well-described example of using SRS with related bioinformatics systems, see http://www.be.gbif.net/services/Documents/DADI_Text by Robert Herzog for the GBIF (global biodiversity information facility). Because of its established high value for processing biology databases, we plan to keep SRS as an alternate in GISR, and work out FlyBase-specific uses over the coming year, while developing an open-source GISR module based on Lucene. Some final organization is needed and it will be added to www.gmod.org's project bestiary. DGD Data Grid Distribution module ~~~ Progress has been primarily in testing Web Services and LDAP interfaces for distributed search/retrieval from database backend systems. Initial development has been using SRS for backend data access; a Lucene adaptor is under construction for use with the above parts. The primary results of testing show (a) Web Services and LDAP methods are equally capable for retrieving files of data (bulk data transfer), (b) LDAP is 10 to 100 times more efficient than Web Services methods for retrieving objects (e.g. data records with fields that the client can use directly), (c) LDAP has a well defined distributed search/retrieval protocol API, general Web Services lack this, but the developing Grid Services (OGSA-DAI project, www.ogsa-dai.org) which we still need to test are heading toward a standard for distributed search API. Delivery of a functional prototype for this module is planned for the coming quarter of work. Recent hires under this GMOD grant include Paul Poole (firstname.lastname@example.org, 1/2 time since july03, a recent bioinformatics masters graduate) to update euGenes.org data, now a project within Argos, and a bioinformatics masters student as an assistant working on GMOD tools (Vasanth Singan, email@example.com, start sept 03)