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NCBI News
NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION
National Library of Medicine
National Institutes of Health
Volume 3, Issue 1 February 1994
Improving GenBank's Taxonomy Access NCBI Through
World Wide Web
T axonomic classification is an important factor in database organi-
zation, searching, and analysis. With assistance from taxonomy
experts, NCBI has undertaken a comprehensive review of the GenBank
taxonomy in order to correct errors, identify inconsistencies, and incor-
N CBI services are now
accessible through World
Wide Web (WWW). WWW is a
porate new scientific knowledge. The process of rebuilding the taxonomy
rapidly growing network infor-
has involved three steps: (1) developing a software tool for manipulating
mation system that permits easy
taxonomic trees, (2) merging existing taxonomies, and (3) enlisting expert
assistance to review, revise, and maintain the taxonomy. access via hypertextlike links to
factual information and database
The first step was to prepare a merged view of existing taxonomies using searching. The NCBI WWW
TaxMan, a taxonomy database management tool developed by NCBI's server provides both information
Scott Federhen. TaxMan includes a set of functions for merging various about and access to GenBank.
taxonomies into a single structure, cross-mapping trees, and annotating Text searching and BLAST
taxonomy entries. With the taxonomy developed by Andrzej Elzanowski sequence similarity searching are
for PIR-International as a foundation, taxonomies from other comprehen- provided as well as access to
sive sequence databases (GenBank, EMBL, Swiss-Prot, and DDBJ) were Network Entrez, which includes a
added and merged. Next, specialized taxonomies such as the ICTV inter- subset of MEDLINE citations
national standard taxonomy for viruses, the U.S. Department of Agricul- related to molecular sequence
ture taxonomy for plants, and the FlyBase taxonomy for Drosophilidae data.
were added at the appropriate branches of the emerging tree.
The search services are front-ends
Following this integration phase, Mitchell Sogin of the Marine Biological to existing NCBI search systems,
Laboratory at Woods Hole organized a workshop to review and revise the and their interfaces should be
taxonomy and to discuss mechanisms for continued maintenance as new considered experimental. NCBI
species enter the database and taxonomic consensus develops. The work- expects to be making changes to
shop included representatives (see box on page 7) specializing in different
v
Continued on page 2
branches of the taxonomic tree.
The taxonomy revision will proceed in two stages. First will be the task to IN THIS ISSUE
formalize the use of organism names in the database by collecting all the
variant spellings, synonyms, and misspellings and then selecting a pre- GenBank's Taxonomy ....................... 1
ferred scientific name for each organism. Second will be a phase-in of new Access NCBI Through WWW .......... 1
taxonomic classification lines from the revised tree as the review of sub- New STS Database, Division ............ 2
trees by participating scientists is completed. Congruently, the GenBank CD-ROM Entrez Expands ................. 3
NCBI Data by FTP ............................ 3
database will be retrofitted with the new classification lines. Subsequent Recent Publications ........................... 4
revisions will reflect new work in the field as well as the addition of GenBank: Focus on Quality ............. 4
synonyms and the correction of misspellings in organisms as they are Frequently Asked Questions ............. 5
NCBI's Board .................................... 6
identified. NCBI Services ................................... 8
Continued on page 7
v
NCBI Creates New Database,
New GenBank Division for STS Data
NCBI News N CBI is creating a new database and a new GenBank division to
facilitate access to the growing body of sequence tagged site (STS)
data being generated by genome mapping laboratories. An STS is a short
NCBI News is distributed three times a DNA sequence that has a single occurrence in the genome of an organism,
year. We welcome communication thus serving as a physical mapping landmark.
from users of NCBI databases and
software and invite suggestions for
articles in future issues. Send corre-
GenBank currently contains about 3,200 STS sequences, most of which
spondence and suggestions to NCBI come from human sources. Beginning with Release 82.0 (April 1994),
News at the address below. STSs will be consolidated into a new division. This reorganization will
facilitate cross-comparison of STSs with sequences in other divisions for
NCBI News
National Library of Medicine
the purpose of correlating map positions of anonymous sequences with
Bldg. 38A, Room 8N-803 known genes.
8600 Rockville Pike
Bethesda, MD 20894 In addition, a separate STS database, dbSTS, will be maintained to manage
Phone: (301) 496-2475 this special class of sequences and provide detailed information about the
Fax: (301) 480-9241
E-mail: info@ncbi.nlm.nih.gov STS map locations and PCR conditions. Following the model of dbEST,1
dbSTS will be a dynamic resource. Sequence similarity searches against
other divisions of GenBank will be performed on a frequent periodic basis,
Editors and the annotations in the STS database will be updated automatically.
Dennis Benson
Barbara Rapp
Methods are under development to enable queries of dbSTS by chromo-
somal and subchromosomal location. Access will initially be by an e-mail
Design Consultant server.
Troy M. Hill
STS data may be submitted to GenBank via e-mail to the address
Photography
Karlton Jackson bulk-sub@ncbi.nlm.nih.gov. Because STSs are usually submitted as a set
of many sequences, we have designed a simple tagged "flat file" format
Editing, Graphics, and Production (available on request) to simplify and streamline the direct submission
Veronica Johnson process. Upon receipt of STS data, GenBank accession numbers will be
Wendy B. Osborne
issued and the data will then be released to the public unless the submitter
In 1988, Congress established the requests that it be kept confidential until publication.
National Center for Biotechnology
Information as part of the National To obtain a copy of the data input format specification or for further
Library of Medicine; its charge is to
information, contact GenBank User Services at info@ncbi.nlm.nih.gov or
create automated systems for storing
molecular biology, biochemistry, and (301) 496-2475.
genetics data, and to perform research 1Boguski, MS, TMJ Lowe, and CM Tolstoshev. dbEST --database for "expressed
into computational molecular biology.
sequence tags." Nature Genet 4:3323, 1993. s
The contents of this newsletter may be
reprinted without permission. The
mention of trade names, commercial WWW, continued from page 1
products, or organizations does not
imply endorsement by NCBI, NIH, or the interfaces and to add more data following evaluation of user feedback
the U.S. Government. and system performance.
NIH Publication No. 94-3272
WWW has client interfaces available at no cost for PC, Macintosh, Unix,
ISSN 1060-8788 and other systems. You can get additional information and client software
(e.g., NCSA Mosaic) by Anonymous FTP to NCSA: ftp.ncsa.uiuc.edu in
the /Web directory. For those familiar with WWW, the URL for
establishing a link to NCBI is as follows: http://www.ncbi.nlm.nih.gov. s
2 NCBI News · February 1994
Entrez on CD-ROM Expands
To Accommodate Growth NCBI Data by FTP
NCBI maintains a repository of
T he sequence databases double in size about every 20 months. To
accommodate this rapid growth, Entrez expanded from one disc to two
in February 1993. With Release 8.0 in December 1993, another organiza-
molecular biology databases and
software development tools that are
publicly available for network users
tional change was required. Prior to December, the Entrez: Sequences through Internet FTP (file transfer
disc contained the sequence database entries plus associated MEDLINE protocol). The available directories
include "repository", "toolbox", and
references and abstracts--approximately 50,000 records in October. A "pub".
larger MEDLINE subset (about 150,000 records) was contained on the
Entrez: References disc. In December all of the MEDLINE data were The repository directory holds more
segregated on the Entrez: References disc to provide more room for growth than 20 databases, such as
of the sequence databases. · Swiss-Prot (Amos Bairoch)
· ACeDB: A C. elegans
Because the Entrez software was modified to accommodate this change in Database
data location, users were required to reinstall the Entrez software with (J. Thierry-Mieg, R. Durbin)
Release 8.0. You can continue to use both discs with a single CD-ROM · FlyBase (Michael Ashburner)
drive by specifying "Disc Swapping," which is now the default option, in · Eukaryotic Promoter
the configuration program, EntrezCf. Entrez will prompt you to insert the Database (Philipp Bucher)
appropriate disc as you search the sequence and reference databases. If · REBASE (Restriction En-
zyme Database - Richard
your computer has two CD-ROM drives, Entrez makes it easy to use them Roberts)
both, with no need to exchange CD-ROM discs.
· CarbBank/CCSD
Entrez on Three Discs in October 1994 · PROSITE (Dictionary of
Protein Sites and Patterns -
Given the rate of growth of the sequence databases, it is clear that by Amos Bairoch)
October 1994 it will no longer be possible to contain all the data on two
The toolbox directory contains a set
discs. Consequently, Entrez will expand to three discs at that time. Our of software and data exchange
projections are that three discs will be sufficient to hold the data until specifications that are used by NCBI
October 1995. to produce portable software, and
includes ASN.1 tools and specifica-
tions for molecular sequence data.
What does this change mean for Entrez subscribers? First, there will be a
price increase to account for production of the third disc. Pricing is The pub directory offers public-
determined each spring by the U.S. Government Printing Office. Based on domain software, such as BLAST (a
past experience, however, it is likely that the increase in price will be quite sequence similarity search pro-
gram), MACAW (a multiple
modest, probably about $20 more per year. The second and more profound sequence alignment program), and
impact will be on hardware requirements. Authorin submission software for
Mac and PC systems.
Options for Accommodating Growth
All data in these directories can be
Users will have at least four ways to accommodate the additional storage transferred through Internet by
requirements of Entrez this October: using the Anonymous FTP program.
To connect, type: ftp
ncbi.nlm.nih.gov or ftp
1. Install a total of three CD-ROM drives on your Mac or PC. A number 130.14.25.1. Enter anonymous for
of manufacturers now offer "tower" type CD-ROM configurations, which the login name, and enter your e-
can accommodate three or more CD-ROM drives. Alternatively, for mail address as the password.
Macintosh users and for PC users who have SCSI host adapters, three Change directories to "repository"
to download databases (cd reposi-
internal and/or external SCSI CD-ROM drives may be "daisy-chained" tory), "toolbox" to download ASN.1
together. With the cost of high-performance "double-speed" SCSI CD- tools (cd toolbox), or "pub" to
ROM drives approaching $300, this approach is the most economical. download public-domain software
(cd pub).
v
Continued on page 6
NCBI News · February 1994 3
GenBank: Focus on Quality
Selected Recent
Publications by
NCBI Staff N CBI continues to concentrate on improving GenBank quality.
Several steps have been taken to correct errors, reduce redundancy,
promote consistency, and ensure the quality of data at the point of entry
Boguski, MS, TMJ Lowe, and CM into the system.
Tolstoshev. dbEST--database for
"expressed sequence tags." Nature Controlling Quality of New Direct Submissions
Genet 4:3323, 1993.
Quality control begins with NCBI's applied database staff. GenBank anno-
Claverie, JM. Detecting frame shifts tators who build and maintain the database entries are trained in molecular
by amino acid sequence comparison. biology and skilled in database production operations. Senior scientists
J Mol Biol 234:114057, 1993.
provide daily scientific guidance and review.
Rudd, KE. Maps, genes, sequences,
and computers: an Escherichia coli When a new submission arrives at NCBI on disk or by e-mail
case study. ASM News 59(7):33541, (gb-sub@ncbi.nlm.nih.gov), an annotator assigns a GenBank accession
1993.
number after a quick review of format and general content. However,
Koonin, EV, and TV Ilyina. before the submitter receives the full GenBank record for review and
Computer-assisted analysis of the comment, the sequence is screened against GenBank using BLAST to
relationships between protein and identify full or partial matches, followed by a search to detect vector con-
DNA sequences involved in rolling
circle DNA replication. Biosystems tamination. Algorithms that check for internal consistency are used to con-
30:24168, 1993. firm coding regions, detect open reading frames, and verify amino acid
translations. Using GenBank content and data representation guidelines,
Wootton, JC, and S Federhen.
Statistics of local complexity in amino
annotators then review the descriptive parts of the entry; assign the locus
acid sequences and sequence name, definition line, keywords, and taxonomy classification; and, in
databases. Comput Chem 17:14963, consultation with the submitter, add and modify features if needed.
1993.
Reducing Redundancy and Regularizing Features
Koonin, EV, and VV Dolja.
Evolution and taxonomy of positive- Although staff at the international DNA sequences databases have been
strand RNA viruses: implications of
comparative analysis of amino acid working together to remove duplicate entries and merge records where
sequences. Crit Rev Biochem Mol appropriate, analyses by NCBI researchers reveal that there is still consid-
Biol 28:375430, 1993. erable internal redundancy in the database: more than 5 percent of the
entries have duplicate sequences and another 5 percent have close matches.
Lawrence, CE, SF Altschul, MS
Boguski, JS Liu, AF Neuwald, and There are also many records that contain coding sequences with no fea-
JC Wootton. Detecting subtle tures, translations, or protein product names. A project to create an
sequence signals: a Gibbs sampling enhanced view of GenBank, called GenBank Select, aims to reduce redun-
strategy for multiple alignment.
Science 262:20814, 1993. dancy and regularize feature annotation. For example, where exact or
nearly exact matches exist between Swiss-Prot and translated GenBank
Gregory, PE, DH Gutmann, entries, the Swiss-Prot translations, names, and descriptions will be substi-
A Mitchell, S Park, M Boguski, tuted in the GenBank records. In addition, subset sequences that exist as
T Jacks, DL Wood, R Jove, and FS
Collins. Neurofibromatosis type 1 separate GenBank entries, such as identical cDNAs or a cDNA and its
gene product (neurofibromin) corresponding genomic sequence, will be merged into a single record for
associates with microtubules. Somat the view presented in GenBank Select. Thus, GenBank Select will be an
Cell Mol Genet 19:26574, 1993.
optional view of GenBank data, which will continue to be distributed and
Major, F, D Gautheret, and accessed as before.
R Cedergren. Reproducing the three-
dimensional structure of a tRNA Keeping Current
molecule from structural constraints.
Proc Natl Acad Sci U S A 90:9408 With support from the National Library of Medicine's MEDLINE indexers,
12, 1993.
who review more than 3,500 journals, GenBank annotators scan the current
v
Continued on page 7
4 NCBI News · February 1994
Q
&
A
I am in a hurry to submit a
sequence, but I don't have a copy
of Authorin. Is Authorin available
electronically for downloading?
Frequently Asked Questions
Authorin is available by Anonymous FTP through the Internet. You will
find the Mac version (3.0) in the /pub/authorin/mac directory and the DOS
version (1.2) in the /pub/authorin/dos directory. If you would like a printed
copy of the documentation or have any questions, contact us at
authorin@ncbi.nlm.nih.gov.
Authorin Macintosh release 3.0 This problem occurs when the path to the ASNLOAD folder is not proper-
crashes at the end of the "Prepare ly specified during the Authorin installation procedure. The ncbi.cnf file
Submission" process and may or must be edited to reflect the user's hard disk name and any possible inter-
may not flash an error message vening folders. If this step is not carried out when following the
and produce an .sbt submission installation instructions, the system may crash when preparing data for
file. What is the problem? submission.
I need an accession number for an The fastest way to get an accession number is to send the Authorin
article that was accepted for submission file (the file ending in the extension .sbt) by e-mail to
publication and I am in a hurry. gb-sub@ncbi.nlm.nih.gov. The accession number will be issued within
How long does it take? 24 hours and e-mailed back to the address from which the submission was
sent.
After loading my Authorin 2.1 You are trying to use Authorin 2.1 with System 7.0x on the Macintosh.
program on the Mac, it crashes With System 7.0x you must use the latest version of Authorin, Release 3.0.
when I begin, gives the following This release will work on both System 6.0x and 7.0x.
error message TXCL_UNLOCK,
and will not let me continue. Why
does this happen?
I have numerous submissions to You can create a template file with the information that will be the same in
make and much of the data is the all the submissions. By opening the template file and saving under a new
same. Do I have to retype author name, you can retain the master file and add additional information to the
and citation information for each new file. Directions are provided in both the Mac and PC manuals for
submission? creating and using a template file.
The term e-mail server is used to The e-mail (electronic mail) servers at the NCBI are host computers that
describe the RETRIEVE and receive specifically formatted e-mail queries, process these queries, and
BLAST e-mail addresses, but I return the search results to the address from which the message was sent.
don't understand exactly what this No specific password or account is needed only the ability to send e-mail
term means. to an Internet site. s
NCBI News · February 1994 5
Entrez Expands, continued from page 3
NCBI's Board Invites
Community Comment 2. Install Entrez index files on the hard disk and use two CD-ROM
drives for the datafiles. The design and organization of the three-
disc Entrez product is not yet complete (more details will be avail-
T he NCBI--and all research centers
at the National Institutes of
Health--has a Board of Scientific
able in the next NCBI News). But we expect that it will be possi-
ble to put all the index files and other files necessary to locate
sequence and reference records on one CD-ROM disc, leaving the
Counselors (BOSC). The Board meets
data records on the remaining two discs. Therefore, users who can
regularly to review NCBI activities and
dedicate approximately 500 MB of magnetic disc space to Entrez
to provide guidance and advice on how
will be able to copy the index and link files to a hard disk and use
best the Center can meet the needs of
two CD-ROM drives to hold the databases. With hard disk costs
the molecular biology community.
less than $1 per megabyte, this alternative is only slightly more
The eight-member board consists of expensive than having three CD-ROM drives and will provide a
molecular biologists and computer considerable improvement in performance.
scientists from academia and industry.
3. For the best performance, use the CD-ROMs only as distribu-
At their most recent meeting, BOSC
tion media and put all the data on magnetic disks. Two gigabytes
members, listed below, invited input
of hard disk storage should accommodate Entrez through October
from the user community on NCBI
1995. Two gigabyte SCSI drives currently cost less than $2,000,
databases, software, and services.
and 16-bit SCSI-2 host adapters for PCs cost about $250. Users
Robert T. Sauer, Ph.D. (Chairman) with newer Macintoshes or Unix workstations should already have
Department of Biology
Massachusetts Institute of Technology the necessary disk controller. Thus, for a cost of about $2,000,
Phone: (617) 253-3163 PCs, Macs, or Unix systems can hold all of Entrez on magnetic
Helen M. Berman, Ph.D. disk. The performance of these systems should be more than
Center for Computational Chemistry adequate for use as departmental servers on local area networks.
Rutgers University
Phone: (908) 932-4667
E-mail: berman@dnarna.rutgers.edu 4. For users with direct Internet connections, Network Entrez is
Charles R. Cantor, Ph.D. available at no cost. As discussed previously in the NCBI News
Center for Advanced Biotechnology (August 1993), Network Entrez requires that a local network
Boston University administrator take responsibility for (1) establishing and maintain-
Phone: (617) 353-8504
E-mail: crc@buenga.bu.edu ing the Internet connection, (2) installing the necessary network
John R. Devereux, Ph.D. software (MacTCP for Macintosh or one of several TCP/IP
Genetics Computer Group, Inc. software packages for Windows PCs), and (3) installing the
Phone: (608) 231-5200 retrieval software (available via Anonymous FTP from
E-mail: devereux@gcg.com
ncbi.nlm.nih.gov). For more information about Network Entrez,
Paula Fitzgerald, M.D., Ph.D.
Merck Research Laboratories send electronic mail to net-info@ncbi.nlm.nih.gov. Users with
Phone: (908) 594-5510 Internet access who do not have the local support necessary for
E-mail: paula_fitzgerald@merck.com Network Entrez can use a version of Entrez that has been adapted
Michael W. Hunkapiller, Ph.D. for use with the Mosaic/World Wide Web hypertext-based
Applied Biosystems Division
information service (see related article on page 1).
Perkin-Elmer Corporation
Phone: (415) 570-6667
Sung-Hou Kim, Ph.D. The expansion of the sequence databases is an inevitable reflection
Melvin Calvin Laboratory of the rapid progress in gene and protein sequencing. An
Lawrence Berkeley Laboratory additional CD-ROM drive or hard disk is the cost of ready local
Phone: (510) 486-4333
access to more than a gigabyte of sequence and related biblio-
Myra N. Williams, Ph.D.
Glaxo, Inc.
graphic data. Contact us via e-mail at info@ncbi.nlm.nih.gov, or
Phone: (919) 990-5686 by phone at (301) 496-2475, if you have any questions about up-
E-mail: mnw30117@glaxo.com s coming releases of Entrez on CD-ROM. s
6 NCBI News · February 1994
Taxonomy, continued from page 1 Focus on Quality, continued from page 4
In addition, taxonomy revisions journal literature to locate new sequences, update publication information,
are now being incorporated into and identify GenBank sequences that should be released to the public
Entrez. With Release 10.0, you database.
will be able to use the organism
field to restrict searches to any In addition, retrospective projects to release published sequences and sys-
level in the taxonomic hierarchy, tematically update the numerous "in press" entries with full citation data are
not just the genus and species under way.
level. For example," eukaryotes,"
"fungi," and "primates" will all be Although only the submitting scientist is permitted to modify sequence data
valid search terms. or annotations, NCBI encourages all GenBank users to point out possible
errors or omissions, provide updated publication information, or request the
From its inception, the taxonomy release of data that have been published. Send update notices to
review has been a collaborative update@ncbi.nlm.nih.gov. s
project. Representatives of the
major sequence databases and
taxonomy experts will continue to
work together to maintain a
current and accurate taxonomy Taxonomy Project Participants
resource. The international DNA
Robert Baker, Texas Tech. University Shung-Chang Jong, American Type Culture
sequence databases, EMBL and Lois Blaine, American Type Culture Collection
DDBJ, have agreed in principle to Collection Eugene Koonin, NCBI
Russell Chapman, Louisiana State University Gary Olsen, University of Illinois at Urbana-
adopt the revised taxonomy as a Michael Donaghue, Smithsonian Institution Champaign
database standard. We invite your Andrzej Elzanowski, PIR-International Kate Rice, EMBL
David Freshwater, University of Miami Hugh Robertson, University of Illinois at
suggestions and participation. Urbana-Champaign
John Gunderson, Marine Biological Laboratory
Anyone interested in more at Woods Hole Mitchell Sogin, Marine Biological Laboratory
at Woods Hole
information or in curating a David Hillis, University of Texas
John Taylor, University of California at
Jack Holt, Bergey's Trust
segment of the taxonomy should Rodney Honeycutt, National Science
Berkeley
Ward Wheeler, American Museum of Natural
contact Scott Federhen at NCBI Foundation
History
(federhen@ncbi.nlm.nih.gov).
TO RECEIVE INFORMATION FROM NCBI, PLEASE SEND THIS FORM TO:
NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION
National Library of Medicine
National Institutes of Health Queries about services and software may also be sent via
electronic mail to info@ncbi.nlm.nih.gov or by fax to
Bldg. 38A, Room 8N-803 (301) 480-9241.
8600 Rockville Pike
Bethesda, MD 20894
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Comments
NCBI News · February 1994 7
NCBI Services
CD-ROM Products Network Access
Entrez: Sequences GenBank Submissions
Integrated sequence data from GenBank, EMBL, DDBJ, Swiss-Prot,
PIR, PRF, and PDB linked to MEDLINE abstracts. Text retrieval New Submissions gb-sub@ncbi.nlm.nih.gov
software for Macintosh and PC-compatible systems running
Windows 3.1 is included, but there is no sequence similarity search Corrections/Updates update@ncbi.nlm.nih.gov
software.
Submission Software authorin@ncbi.nlm.nih.gov
NCBI-GenBank (Flat File)
GenBank Internet Access
Data distribution disc containing the GenBank DNA database
in flat file format. No software included. E-mail Servers retrieve@ncbi.nlm.nih.gov
blast@ncbi.nlm.nih.gov
NCBI-Sequences (ASN.1)
Network Entrez net-info@ncbi.nlm.nih.gov
Data distribution disc containing the Entrez: Sequences integrated
sequence dataset in the ASN.1 standard data description format. Anonymous FTP ncbi.nlm.nih.gov (130.14.25.1)
Intended primarily for software developers. No software included.
Directories for GenBank current
release and daily updates:
CD-ROM Orders
genbank (full releases)
To place orders with the Superintendent of Documents (U.S. genbank/daily (cumulative)
Government Printing Office), phone (202) 783-3238 or genbank/daily-nc
fax (202) 512-2233. To check on orders, phone (202) 783-3238 or (noncumulative)
fax (202) 512-2168
Order forms available from NCBI.
General Information info@ncbi.nlm.nih.gov
DEPARTMENT OF HEALTH AND HUMAN SERVICES
Public Health Service, National Institutes of Health FIRST-CLASS MAIL
National Library of Medicine
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NATIONAL INSTITUTES OF HEALTH · National Library of Medicine
NCBI News
8 NCBI News · February 1994