The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookAbout NCBIPublications
student will submit questions for a classroom assignment, providing a special outreachopportunity to young scientists.
Because of the genetic focus of many of NCBI resources, we receive a number of questionsfrom the general public regarding medical issues. The NCBI Help Desk staff can neitherprovide direct answers to medical questions nor give medical advice or guidance. However,we do provide suggestions on how to search our resources for information on the gene orcondition of interest and refer users to the National Library of Medicine (NLM) customerservice group for further assistance with PubMed (Chapter 2), MEDLINEplus, and
ClinicalTrials.gov. We also refer them to outside organizations that can provide informationon such topics as support groups and sources of medical advice.
Questions about PubMed are handled by a separate customer service group within the NLM.Their direct address is custserv@nlm.nih.gov, and their phone number is 1-888-FIND-NLM.PubMed questions that are received at the NCBI Help Desk are forwarded to NLM.
Development of User Support Materials
Because of its ongoing personal contact with our users, the User Services group plays animportant role in communicating with database development and production teams, makingsuggestions, testing new releases and new features, and keeping them informed of problemsthat people are having with the services. The team also collaborates with developers in creatinghelp documents, frequently asked questions (FAQs), tutorials, and workshop materials.
Tutorials on the Web
Web-based tutorials for BLAST, Entrez, Cn3D, and PubMed are currently available, withadditional topics under development. Tutorials are produced on a collaborative basis bydatabase development and User Services staff.
In keeping with the “plain language initiative” at NIH, the About NCBI section of the NCBIWeb site presents many fundamentals of NCBI's bioinformatics tools and databases, includinga science primer covering such topics as molecular genetics, genome mapping, SingleNucleotide Polymorphisms (SNPs) (Chapter 5), and microarray technology (Chapter 6). Amodel organism guide presents various model organisms and their uses in laboratory settings.As an introduction and orientation to NCBI's multifaceted Web site, the About NCBI sectionappeals to the general public, educators, and researchers alike.
NCBI Site Map
The NCBI Site Map serves as a guide to NCBI resources. It provides a comprehensive, linkedlist of resources, along with a brief description of each resource. An effective way to locate aresource of interest within the Site Map is to perform a Find in Page search, a function that isbuilt into all commonly used Web browsers.
The NCBI News is a quarterly newsletter that includes articles on new services, new features,and basic research at NCBI, as well as how to use selected resources for common applications.The newsletter is available free of charge and is offered online and by print subscription.The User Services group also prepares fact sheets, brochures, and other public informationmaterials to describe and illustrate NCBI services. A list of available materials is provided inthe About NCBI section of the Web site, under News.
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The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookOverview articles entitled GenBank and Database Resources of the NCBI have also beenpublished recently in the annual database issues of Nucleic Acids Research (1-3).
Outreach
NCBI's continuing emphasis on outreach to the scientific community is evident in its
multifaceted program that includes exhibiting its services at scientific meetings, offering avariety of training courses, and developing Web-based tutorials and workshops.
Exhibits at Scientific Meetings
NCBI exhibits at approximately 15 scientific meetings per year, providing an opportunity fora wide range of researchers, students, and teachers to see demonstrations of NCBI resourcesand interact directly with NCBI staff. The current exhibit schedule is posted on the NCBI Website in the About NCBI section, under NCBI at a Glance.
Workshops are offered at select scientific meetings and include the standing workshops
described below in the Training section, but workshops also can be customized for particularaudiences. Meeting organizers who would like to invite NCBI to offer a workshop areencouraged to do so.
Training Courses
NCBI has a growing training program consisting of full-day, half-day, and two-hour coursesthat are usually a combination of lecture and computer-based formats. There are also advancedcourses that are given over a more extended time period. Each is described briefly below, andfurther information on the training programs can be found in the Education section of the Website, under NCBI Courses.
A Field Guide to GenBank and Other NCBI Resources
A Field Guide to GenBank and NCBI Molecular Biology Resources is a training course offeredin a lecture format, followed by hands-on computer sessions. It is designed as a basic but broadintroduction to NCBI tools and resources.
Field Guide topics include the following: description and scope of the primary database,GenBank (Chapter 1); derivative databases, such as UniGene (Chapter 21), Entrez Gene(Chapter 19), and Reference Sequence (RefSeq) (Chapter 18); effective database searchingusing Entrez; NCBI structure databases and the structure viewer, Cn3D; sequence similaritysearching using the BLAST programs; the Conserved Domain Database (CDD) and associatedsearch engine; and genome resources, including the NCBI assembly of the draft humangenome, access to both finished and unfinished microbial genomes, and the genome MapViewer.
The course is offered by invitation at academic institutions as well as at selected scientificconferences. If you are interested in hosting a course at your institution or conference, writeto info@ncbi.nlm.nih.gov, and your request will be routed to the course coordinator.The course is also offered four times a year at the NLM on the NIH campus in Bethesda,Maryland, and is free and open to anyone who would like to attend.
More information on this course is available in the Education section of the NCBI Web site,under NCBI Courses. The Web site includes the course handout, slide presentations, andproblem sets with answers. A schedule of planned courses at NLM and elsewhere is postedunder Upcoming Courses.
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The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookMolecular Biology Information Resources
This course is designed primarily for medical and science librarians or other professionals whoare providing support services for molecular biology information resources. It provides anintroduction to four categories of molecular biology information available from NCBI:
nucleotide sequences, protein sequences, three-dimensional structures, and complete genomesand maps. An overview of search systems available at the NCBI, particularly Entrez andBLAST, emphasizes how search skills related to other types of information resources alsoapply to molecular biology databases. The course concludes with a discussion of various levelsof molecular biology information services provided by librarians.
The Medical Library Association approves this course for eight continuing education credithours. The course has been given at 24 locations since May 1997. Because of the increase inNCBI services, courses are being revised and are not being scheduled at this time.
More information on this course is available in the Education section of the NCBI Web site,under NCBI Courses. The Web site includes the course materials used for the lecture and a setof exercises.
NCBI Advanced Workshop for Bioinformatics Information Specialists
A new 5-day advanced course on NCBI resources has been developed as part of a collaborativeproject with a group of scientists and librarians who currently provide bioinformatics supportservices at their universities. The course provides detailed descriptive information as well ashands-on experience with handling a wide range of user questions. The course is designed forbioinformatics support staff based in university medical libraries so that they can, in turn, assiststudents, faculty, staff, and clinicians at their institutions in the use of molecular biologyinformation resources. Additional information on this course is available in the Educationsection of the NCBI Web site.
Specialized Mini-Courses
The Service Desk staff also offers four mini-courses: BLAST QuickStart, Unmasking Genesin the Human Genome, Making Sense of DNA and Protein Sequences, and GenBank andPubMed Searching. Each is described briefly below. The purpose of the mini-courses is tofocus on specific research application areas and address how to use multiple NCBI resourcestogether to answer a research question. Additional problem-oriented mini-courses are underdevelopment.
The courses are 2 hours each in length. An overview is given during the first hour in lectureformat, followed by a 1-hour hands-on session. Although primarily given on the NIH campus,NCBI is beginning to offer these workshops at outside institutions as well. Although the mini-courses were originally designed to be presented by an instructor, they are constructed in anonline notebook format; therefore, it is possible to take the course on your own. Revisions toaugment the online notebooks with lecture material and make the courses completely self-guided are currently under way.BLAST QuickStart!
This mini-course is a practical introduction to the BLAST family of sequence-similarity searchprograms. Exercises range from simple searches to creative uses of the BLAST programs.Unmasking Genes in the Human Genome
This mini-course covers how to find genes, promoters, and transcription factor-binding sitesin human DNA sequences. It is designed around a program developed within User Services
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The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookCoreBio
called Greengene, which integrates the output of several gene-finding tools and allows a codingsequence and accompanying protein translation to be assembled from the exons detected bythese programs. Because the output of several programs is integrated, there is increasedreliability in exon selection.
Making Sense of DNA and Protein Sequences
In this course, participants find a gene within a eukaryotic DNA sequence. They then predictthe function of the derived protein by seeking sequence similarities to proteins with
documented function using BLAST and other tools. Finally, a 3D modeling template is locatedfor the protein sequence using the Conserved Domain Search (CDD-Search).
During the first hour, an instructor walks the class through an analysis of an uncharacterizedDrosophila melanogaster genomic sequence from a GenBank record. During the second hour,participants perform the same analysis independently, using a different genomic sequence.GenBank and PubMed Searching
This mini-course provides an overview of literature searching and sequence retrieval using thePubMed and Entrez database search interfaces. Exercises illustrate advanced search tips forusing Entrez, many of which explore the use of the Preview/Index options for specifyingparameters to limit the search results. The course also features 21 self-scoring exercises forGenBank.
The NCBI Learning Center
In addition to communication by email and phone provided through the Help Desk, a regularresearch consultation service provides one-on-one support for researchers in the NIH
community. The consults are available by appointment and are provided in 1-hour time slotsat the NIH Library as well as the NCBI training facility. Because of the success of the program,this type of service may be offered by appointment at selected scientific meetings in the future.
An innovative training program that began in 2001 aims to train molecular biologists for a newtype of career as bioinformatics specialists who provide institutional support for users ofcomputational biology tools. The NCBI Core Bioinformatics Facility (referred to as theCoreBio program) currently functions to train and support a network of bioinformatics
specialists serving individual Institutes at NIH. NCBI's CoreBio facility trains Core membersidentified by their respective institutes in the use of its bioinformatics tools. The Core members,in turn, support the use of NCBI tools and databases by researchers at their institutes.The training is provided over a 9-week period, with students attending lectures and completingpractical exercises in the morning and returning to their regular workplace in the afternoon.The coursework centers on one major topic each week and follows the rough schedule givenbelow:
WEEK 1: Introduction to the Sequence DatabasesWEEK 2: BLAST
WEEK 3: The Human GenomeWEEK 4: Genomic BiologyWEEK 5: Molecular Modeling
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The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookWEEK 6: Web Page DevelopmentWEEK 7: Setting Up a BLAST Web ServerWEEK 8: Interaction with UsersWEEK 9: Practicum
During week 9, the students pursue an institute-related project with the assistance of NCBIinstructors. These projects run the gamut from the compilation of specialized datasets and datamining to the creation of novel BLAST interfaces and the construction of new data displaytools. Students also develop a Web page to support the services they are developing for therespective Institutes at the NIH.
Although currently a NIH-based program, other organizations are welcome to consider usingthe program as a model for development of similar initiatives to meet their bioinformaticssupport needs.
Conclusion
At NCBI, we encourage our users to contact us with questions, suggestions, and requests fortraining or presentations on NCBI services. We invite feedback on tutorials, FAQs, and othersupport materials and welcome suggestions regarding additional materials that would be usefulin guiding users through the wide range of services offered by NCBI.
References
1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. GenBank. Nucleic AcidsRes 2002;30:17–20.99127 [PubMed: 11752243]
2. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM,Tatusova TA, Wagner L, Rapp BA. Database resources of the National Center for BiotechnologyInformation: 2002 update. Nucleic Acids Res 2002;30:13–16.99094 [PubMed: 11752242]
3. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM,Tatusova TA, Wagner L, Rapp BA. Database resources of the National Center for BiotechnologyInformation. Nucleic Acids Res 2001;29:11–16.29800 [PubMed: 11125038]
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