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1.    DATABANK CREATED  BY  NICED  LIBRARY:

         We  live in a society that is rapidly changing due to amazing advances in communications and technology. These changes are accompanied by an extreme proliferation of information in both print and electronic formats-what some are calling an “information explosion”.

          Overabundance of information has been referred to as “data smog” is that it contributes  to a sense of overwhelming anxiety deriving from having to make decisions without having ALL the information available. Today’s Librarian must be able to recognize when information is needed and have the ability to locate, evaluate and use effectively the needed information.

           To cope effectively with data smog, researchers/scientists must become discerning users of information. Hence  NICED  Library  has  created  databank  to  organize  information  on  particular  topics  like HIV, HIV1, HIV2, Cholerae etc.

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    Database Directories and Lists:

The large number of databases (collected from Internet) naturally leads to the impulse to create database directories and lists. Many of the comprehensive web sites listed in this guide also provide such lists and are worth consulting.

NCBI's Entrez Global Query is a cross-database search option that searches many Entrez databases at one time. The results list the number of records in each database that match your query, and provides links to those records, but unfortunately doesn't let you combine the results into a single set for review or further manipulation. The Global Query search page also acts as a short Entrez database directory since each database is briefly described (select the question mark icon next to each database).

Nucleic Acids Research: Annual Database Issue (January)

For the past twelve years the journal Nucleic Acids Research, published by Oxford University Press, has devoted the first issue of each year to listing and describing the most noteworthy molecular biology and bioinformatics databases. This issue always includes many informative articles describing selected databases in depth as well as an extensive annotated list of hundreds of databases called the Molecular Biology Database Collection. See also the companion Web Server Issue of this journal, which comes out in July.

Introduction to Molecular Biology Databases

Although not technically a directory, this article, written in 1999, is still a very helpful introduction to the major databases, including many of the organism-specific ones that are outside the scope of this guide. A good starting place for the non-specialist.

Sequence Retrieval System (SRS) database descriptions

This database of database descriptions can be accessed a number of ways. From the Public SRS Servers List you can view an alphabetical list of databases (scroll down past the list of servers at the top to see the list of databases or "libraries" in the middle of the page). Click on the link for the server that is hosting the database you are interested in to view the record for the version of that database as mounted on that server. Or, you can link to the database descriptions from the search interface of a particular server (for example, see the European Bioinformatics Institute server). This method is particularly helpful because here the databases are sorted by database type (e.g., sequence libraries,

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  protein 3D structures, mutations, SNP, metabolic pathways, etc.). Click on the plus sign next to the type to expand the list, then click on the database name to access the description of that database as mounted on that server. You can also go one step further and actually initiate your search in those databases from this page as well.

 Nucleotide Sequences 

GenBank, and Entrez Nucleotides Database

GenBank is the nucleotide sequence database built and distributed by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. Genbank data are obtained through direct submission of sequence data from individual laboratories, from large-scale sequencing projects, and from the US Patent and Trademark Office. GenBank, together with the DNA Databank of Japan (DDBJ) and the European Molecular Biology Laboratory (EMBL) comprise the International Nucleotide Sequence Database Collaboration. These three organizations exchange data on a daily basis. The Entrez Nucleotides database is a collection of sequences from several sources, including GenBank, RefSeq, and PDB. The number of bases grows at an exponential rate. As of April 2004, there were over 38 billion bases in the Nucleotides database.

There are two ways to search: a text-based query can be submitted through the Entrez Nucleotides Database or a sequence query can be submitted through the BLAST family of programs. Searches of the Entrez Nucleotides database query the text and numeric fields in the record, such as the accession number, definition, keyword, gene name, and organism fields to name just a few. So, for example, entering the terms Bacillus anthracis results in records that contain and describe nucleotide or protein sequences related to the anthrax bacteria. Nucleotide sequence records in the Nucleotides database are linked to the PubMed citation for the article in which the sequences were published. Protein sequence records are linked to the nucleotide sequence from which the protein was translated. To become an effective searcher of this database takes study (see the NCBI Education Page).

The most common method of accessing and analyzing the sequence data in GenBank is through a BLAST search of the Nucleotides database. If you have obtained a record

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through a Nucleotides Database search you can read the nucleotide sequence in the record. However, most researchers wish to submit a nucleotide sequence of interest to them to obtain records that match that sequence with a high probability of certainty. This is done using the BLAST (Basic Local Alignment Search Tool) programs. You select the BLAST program you wish to use depending upon the type of comparison you are doing (nucleotide to nucleotide, or nucleotide to protein sequence, etc.) and then you select the database to run the query in (any of several nucleotide or protein databases). Many NCBI databases accept BLAST searches, as do many of the other databases covered elsewhere in this guide. You can learn more about BLAST searching from the NCBI BLAST information page.

Entrez Global Query - a cross-database simultaneous search of many Entrez databases, including GenBank.

EMBL Nucleotide Sequence Database

"The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ). Each of the three groups collects a portion of the total sequence data reported worldwide, and all new and updated database entries are exchanged between the groups on a daily basis." EMBL is maintained and distributed by the European Bioinformatics Institute (EBI). The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva.

From the home page you can submit simple text searches to the EMBL Nucleotide Sequence Database, or to the Protein Databank (what you search when you select protein structures from the menu) or to a protein sequence database called Swall. For more complex searches, they recommend accessing the databases through the Sequence Retrieval System (SRS) server. SRS is a database querying / navigation system, similar in function to the Entrez system. It allows you to simultaneously search across several databases and to display the results in many ways. SRS can be used to access a large number of databases, including EMBL, SWISS-PROT and the Protein Databank,

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depending upon the configuration of the particular SRS server you are using. The structure and content of an EMBL Nucleotide record is very similar to that of an NCBI Entrez Nucleotide database record.                               

   Genome Databases  :

Entrez Genome

"The whole genomes of over 1000 viruses and 100 microbes can be found in Entrez Genomes. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses and organelles." Text searches can be done from the main page. Data can also be accessed alphabetically by species (see links on left of main page), or hierarchically by drilling down through a taxonomic list to a graphical overview for the genome of that organism, then to specific chromosomes, then on to specific genes. At each level are maps, pre-computed summaries, analysis appropriate to that level, and links to related records from a variety of other Entrez databases. BLAST searches of some genomes are also possible. See also the Entrez Global Query - a cross-database search option that searches many Entrez databases at one time.

In addition, very useful pages for some of the most commonly studied species (e.g., human, mouse, fruit fly, malarial parasite) can be found on the Genomic Biology page. These pages are so detailed that each could be classified as a comprehensive web site in itself. Each one brings together links to the genomic data, useful tools, related data sources and news about the genome of that species. The Human Genome Guide is particularly rich.

Human Genome Browser from UCSC

"The sequence of the human genome is too big to see at all at once; few people want to look at raw DNA sequence anyway. The alternative is the Human Genome Browser for a quick display of any requested portion of the genome at any scale, along with more than two dozen tracks of information (genes, ESTs, CpG islands, assembly gaps, chromosomal band, ...) associated with the complete human genome sequence... Clicking  

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on a displayed feature opens a second window providing protein sequence, coordinates and accession numbers, as appropriate. Clicking in the corner of the display calls up raw DNA sequence corresponding to the display window boundaries. This look-up feature is far more convenient than manual retrieval of a precise coordinate range from GenBank entries."

The Genome Database (GDB)

The Genome Database is the official central repository for genomic mapping data resulting from the Human Genome Initiative. The database contains three types of data: (1) regions of the human genome, including genes, clones, and ESTs,

(2) maps of the human genome, including cytogenetic maps, linkage maps, radiation hybrid maps, content contig maps, and integrated maps (these maps can be displayed graphically via the Web), and

(3) variations within the human genome including mutations and polymorphisms, plus allele frequency data.

There are options to browse genes by chromosome, genes by symbol name, and genetic diseases by chromosome. There are multiple ways to search, including text-based searches for people, citations, segment names or accession numbers, and sequence searching via BLAST.

KEGG: Kyoto Encyclopedia of Genes and Genomes

This database often appears in Google searches, so let's put it in context. Despite the name, this is actually a biochemical pathway database and gene catalog, not an encyclopedia in the book sense. "The primary objective of KEGG is to computerize the current knowledge of molecular interactions; namely, metabolic pathways, regulatory pathways, and molecular assemblies. At the same time, KEGG maintains gene catalogs for all the organisms that have been sequenced and links each gene product to a component on the pathway. Because we need an additional catalog of building blocks, KEGG also organizes a database of all chemical compounds in living cells and links each compound to a pathway component. And finally, KEGG aims at developing new bioinformatics technologies toward functional reconstruction."

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 :: Protein Sequences :

  SWISS-PROT

SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library. "The data in Swiss-Prot are derived from translations of DNA sequences from the EMBL Nucleotide Sequence Database, adapted from the Protein Identification Resource (PIR) collection, extracted from the literature and directly submitted by researchers. It contains high-quality annotations, is non-redundant, and cross-referenced to several other databases, notably the EMBL nucleotide sequence database, PROSITE pattern database and PDB. SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and a high level of integration with other databases."

Entrez Protein Database

"The Protein database contains sequence data from the translated coding regions from DNA sequences in GenBank, EMBL and DDBJ as well as protein sequences submitted to PIR, SWISS-PROT, PRF, and the Protein Data Bank (PDB) (sequences from solved structures)." However, as previously mentioned, the native SWISS-PROT records usually contain more detailed annotations than will be obtained from Entrez Protein Database records derived from SWISS-PROT records. In typical Entrez fashion, results from a search of the Protein database will link to PubMed, to the taxonomy database, to related sequences, and in some cases to pre-computed BLAST search results (look for BLink links) when available. See also the Entrez Entrez Global Query - a cross-database search option that searches many Entrez databases simultaneously.

Protein Information Resource - International Protein Sequence Database (PIR-PSD)

In 1988 the Protein Information Resource (PIR), which is affiliated with Georgetown University Medical Center, established a cooperative effort with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID) to collect, publish and distribute the PIR-International Protein

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Sequence Database (PIR-PSD). They describe the database as "a comprehensive, non-redundant, expertly annotated, fully classified and extensively cross-referenced protein

sequence database in the public domain". Text searches can be done in the title, species, author, citation, keyword, superfamily, feature and gene name fields. Gapped-BLAST sequence similarity searches are also an option. Note that both SWISS-PROT and the Entrez Protein database contain data adapted from the PIR.

      Protein Structure  :

Protein Data Bank (PDB)

The PDB was established at Brookhaven National Laboratories in 1971, making it the first public bioinformatics database. The PDB is now operated by the Research Collaboratory for Structural Bioinformatics (RCSB) which is a collaborative effort of the San Diego Supercomputing Center, Rutgers University, and the National Institute of Standards and Technology (NIST). The PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. It includes a repository of experimentally determined three-dimensional structures of biological macromolecules (proteins, enzymes, nucleic acids, protein-nucleic acid complexes, and viruses) derived from x-ray crystallography and NMR experiments. Approximately 50-100 new structures are deposited each week. A variety of information associated with each structure is available, including "sequence details, atomic coordinates, crystallization conditions, 3-D structure neighbors computed using various methods, derived geometric data, structure factors, 3-D images, and a variety of links to other resources."

·         A narrated tutorial illustrates how to search, navigate, browse, generate reports and visualize structures. [This requires the Macromedia Flash player download.]

MMDB: Molecular Modeling DataBase

The MMDB is NCBI's structure database. It is a subset of three-dimensional structures obtained from the Protein Databank (PDB), excluding theoretical models. MMDB adds value through the addition of explicit chemical graph information and through the cross-linking of structural data to bibliographic information, to the sequence databases, and to the NCBI taxonomy. The explicit bond information makes for more consistent interpretation of the coordinate data by visualization software.

NICED Library, Kolkata

  2. RADIO FREQUENCY  IDENTIFICATION  (RFID) :

According to an initiative of ICMR HQ,  RFID  installation   is  to  be  initiated  in  the 11^th  five  year  plan. With fund available from ICMR HQ, NICED Library will be able to purchase this machine which  will help  further  in  modernization of NICED Library.

BENEFITS  OF  RFID:

 RFID  is  used  to  increase  efficiency  &  reducing  cost  in  Library.  Through  RFID automation  &  self-service  can  be  achieved  in  Libraries.  Added  advantage  is  that  through  RFID   security  can  be  provided  to  different  media  in  Libraries. The  system  is  reliable  can  be  easily  operated  &  flexible. There  is  no need  for  an additional  server   which   means   that   products   can   be   connected   easily   to   a   library’s  network.

The   core   of   the   system   is   the   RFID   tag ,   which  can   be  fixed  inside  a   book’s front  cover  or  directly  onto  CDs  &  videos. This  technology  uses  radio  communication :  a reader  which  is  integrated  into  a  RFID  check  out  unit,  activates  data   transmission  from  the chip  to   the  library’s  database.  These  tags  can  store  far  more  information  about  an  item.  In addition,  RFID  chips  are read/write  so  that  data  can  be  updated  where ever  necessary.

RFID  also  allows  the  use  of  a  single  label  for  both  circulation  and  security.  When newly  acquired  media  are  entered  into  the  collection,  only  one  intelligent   tag  needs  to  be  attached. This  cuts  manual  effort  per  operation  in  half. RFID  tags  can  be  used  for status  control  as  well  as  for  security  checks. There  is  no  need  for  an  additional  security  stripe.

If  an  unauthorized  user  tried  to  check out  an  item  and  take  it   out  of  the Library  through   the  sensor   gates,  an  alarm  would  be  set  off.  The  sensor  gates  function  as  antennas  and  have  a  reading  distance  of  three  feet  between  them.

Users  can  also  issue  books  to  themselves  using  this  technology,  making circulation  faster  and  easier.  Automatic  book  return  offers  similar  benefits  and  can  optimize  the check-in  process  dramatically. Such  a  device  can  be  passed  along  the  shelves  to  enable  the  inventory  to  be  checked  automatically,  rather  than  handling  each  item  individually.  

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    3. MODERNISATION  OF  NICED  LIBRARY  TURNING  TO  E-LIBRARY

Indian Council of Medical Research (ICMR) HQ, has initiated the trend towards making all the ICMR sister Institute’s Libraries into electronic library. NICED, being one of the sister Institutes has received from ICMR funds, several online databases like PML, Science Direct, OVID . ICMR HQ has provided necessary funds for Library automation software LIBSYS. However funds for retro conversion is not forthcoming. We need necessary funds for bar code scanner also. NICED Library has progressed over the years according to the plans of ICMR and is geared to turn into an e- library.

4. FULL TEXT  NICED PUBLICATIONS: 1964-2004:

NICED  Library  has  compiled  NICED  full  text  publications  of  the  scientists  of  the  Institute  from  1964  till  2004 . The  work  has  been  a  very  huge  one  as  this  required  collection  of  full  text  publication  of  the  scientists  of  the  Institute  as  old as  1964  till  recent  date as instructed by our Director ( now Addl. Dir.  Gen ) Dr. S. K. Bhattacharya. Without his constant help and guidance it was too difficult to complete the laborious job . We have the hard copy as well as the soft copy of the  full text database.

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     5. REFERENCE SERVICE  

    Staff  members of the Center respond to letter, e-mail, and telephone requests for    

    information. The staff provides full reference desk services to the members of the   

    NICED   and medical community, CALCUTTA /JADAVPUR / RABINDRA 

    BHARATI/  KALYANI/ VIDYASAGAR University, the Medical Libraries, the Kolkata   

    Medical  Society, and the general public. We assist in locating library materials and with 

    specific information in  the history of medicine, bibliographic instruction, identification of

    publications and citations, verification of information, obtaining information on holdings

    at this and other institutions, and tours of the collection.

Virtual Reference Desk (VRD) Network [a collaborative Internet-based question and answer service providing support to digital reference (or AskA) services by accepting out-of-scope and overflow questions], but can be applied to all digital reference services and consortia.

The facets are divided into two main categories: user transaction and service development/management. The user transaction category includes those components that occur during the question-answering process (i.e., accessibility, prompt turnaround, clear response policy, interactive, and instructive); these features are generally visible to the user. The service development/management category involves decisions made in creating and maintaining the service that affect overall quality and user satisfaction (i.e., authoritative, trained experts, private, reviewed, provides access to related information, and publicized).

Levels of Quality

Digital reference services differ from each other in many aspects including policy and procedure, subject matter expertise, and available resources. For this reason, it is important that quality criteria accommodate the wide range of possibilities of various services and their readiness to meet certain expectations. Each "facet" is presented at two different levels:

Essential - Required for network membership

Recommendations – current state and goals of membership

All services must fulfill the essential level of requirements for each facet of quality. The recommendations level represents a wide range of possibilities and reflects the current state and goals to which all AskA services in the network will strive to achieve over time.

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