Database cross-reference

To return to the scientific content of the SWISS-PROT database, the next section contains the DR (Database cross-References) lines ... 

This example also illustrates the use of the database cross-reference (db xref). This controlled qualiher allows the databases to cross-reference the sequence in question to an external database (the first identifier) with an identifier used in that database. The list of allowed db xref databases is maintained by the International Nucleotide Sequence Database Collaboration. 

PubChem Substances The PubChem substance database contaius chemical stmctures, synonyms, registration IDs, description, related urls, and database cross-reference links to PubMed, protein 3D stracmres, and biological screening results. We can search deposited chemical substance records using names, synonyms, or keywords. Links are also provided to biological property information and depositor websites. 

A recent survey showed that users were enthusiastic about this new database. Cross reference to CAS Registry Numbers and the capability to search polymers by class and monomer component were perceived as advantages. Comprehensive retrieval at specific and generic levels with controlled terms as well as free text searching of the abstract text and bibliographic data afforded good flexibihty. One command language to search both Du Pont proprietary and STN files was heartily welcomed. 

Recover Database restructures and re-indexes the data. The rebuild process recovers al I key indexes and cross references. 

The change in the cyclic structures, now drawn in the more contemporary notation for which Hampden Data Services are to be thanked continues. The book is also now available as an electronic database, with all the improved ease of searching for cross-references or related materials which that brings. In future, it is proposed to supplement this rather more frequently than the new editions of the book will appear. 

Ultimately, this section is meant to function as a ready-reference database for learning or review of bioconjugate chemistry. In this regard, a reaction can be quickly found, a short discussion of its properties and use read, and a visual representation of the chemistry of bond formation illustrated. What this section is not meant to be is an exhaustive discussion on the theory or mechanism behind each reaction, nor a review of every application in which each chemical reaction has been used. For particular applications where the chemistries are employed, cross-references are given to other sections in this book or to outside literature sources. 

RTECS Registry of Toxic Effects of Chemical Substances number is a unique and unchanging number used to cross-reference the RTECS database, which is a compendium of data extracted from the open scientific literature. Six types of toxicity data are included in each file (1) primary irritation, (2) mutagenic effects, (3) reproductive effects, (4) tumorigenic effects, (5) acute toxicity, and (6) other multiple dose toxicity. 

The system is now made up of a disparate set of components each one keeps a part of the information needed by the whole system. The Accounts in the Accounts system refer to the People in the Contacts database. How do we represent these cross-references ... 

Notice that this is an invariant of the company Sales system design. There is nothing that constrains a Contacts database in general to have cross-references to Accounts databases after all, it s a third-party component. Therefore ... 

They have extensive available database and cross-reference capability for evaluation of relevance to human situations. 

As with the DE lines, the CC lines give an indication about the level of characterization of a protein. The example provides experimentally verified information about the "function", the quatenary structure ("SUBUNIT"), the "SUBCELLULAR LOCATION" and the "TISSUE SPECIFICITY" of the protein. A description of the "disease (s) " known to be associated with a deficiency of the protein, a description of the "SIMILARITY" of the protein with other proteins, and a cross reference to network "DATABASE" resource(s) for this specific protein are also found. 

Description of a cross reference to a network database/ resource for a specific protein... 

The DR lines link SWISS-PROT to other biomolecular databases. SWISS-PROT is currently linked to 29 different databases. The preceding example shows links to 19 different entries in 6 different databases. The cross references allow users to navigate to linked databases to retrieve part or all of the related information. The format of a DR line, except for cross references to PROSITE (Hofmann et al., 1999), Pfam (Bateman et al., 1999), and the EMBL nucleotide sequence databases (Stoesser et al., 1999), is the following ... 

The specific format for cross references to the EMBL nucleotide sequence database is ... 

The ENZYME database (Bairoch, 1996) is also used to generate standardized description lines for enzyme entries and to allow information such as catalytic activity, cofactors, and relevant keywords to be taken from ENZYME and to be added automatically to TrEMBL entries. Additionally, specialized databases such as FlyBase (FlyBase Consortium, 1999) and MGD (Blake et al., 1999) are used to transfer information such as the correct gene nomenclature and cross references to these databases into TrEMBL entries. The automatic analysis and annotation of TrEMBL entries are redone and updated every TrEMBL release. 

The modification of data already on file is accomplished in a somewhat similar manner. The information in the database is first retrieved through one of the query methods and then altered. In the case of invalid data or an unplausable chemical structure, MAECIS also contains a delete function. MAECIS creates and maintains for the user all of the necessary cross-references between the associated data files. 

Synonyms which are found in other databases or in the literature, abbreviations, names of commercially available products. If identical names are frequently used for different enzymes, these will be mentioned here, cross references are given. If another EC number has been included in this entry, it is mentioned here. 

In addition, FSIS has implemented a nationwide interagency computerized information database known as the Residue Violation Information System (RVIS), to review, sort, cross-reference, and manage all residue data obtained by FSIS, FDA, or other agencies from residue violation cases. This includes names and addresses of sellers and producers, dealers, and the results of investigations. 

Finally, I should mention a word about filing technical papers. It is tempting to keep a file of papers by subject, and this is satisfactory for collections of 100 to 200 papers, but beyond that a more systematic method is necessary. Ben Wylie, my dissertation advisor, filed his papers by unique serial number and uses an ingenious system of cross-referenced index cards for retrieving papers by author, title, or subject. I ve adopted the same serial-number system, but I use a computer database to cross reference the file records. I use that database online to help locate a needed reference at a moment s notice. 

Figure 1.16 Relation between the MOS and the cognitive corrected PAQM (PAQMc4.o, wo.i) for the ETSI GSM full rate speech database. Crosses represent data from the experiment based on the modulated noise reference unit, circles represent data from the speech codecs.

The Protein Information Resources (PIR) (Wu et al., 2002) of NBRF in collaboration with MIPS and JIPID produces the annotated protein sequence database in the PIR-MIPS International Protein Sequence Database (PSD). The PSD is a comprehensive annotated and nonredundant protein sequence database. Its annotation includes concurrent cross-references to other sequence, structure, genomic and citatation databases, as well as functional descriptions and structural features. The PIR-International database is accessible at the PIR site, http //pir, georgetown.edu, and at the MIPS site, http //www.mips.biochem.mpg.de. 

Because licensed vaccines are the focus of much attention in the public as well as in the vaccine research community, VIOLIN has two subdatabases that focus on licensed human and animal vaccines. The Huvax subdatabase (http //www.violinet.org/huvax) stores all licensed human vaccines in the USA and Canada. The data for these licensed human vaccines are annotated through manual curation and a vigorous review process. Huvax includes manually curated data including manufacturer, trade name, storage information, age at which the vaccine should be administered, and other relevant information. These vaccines are also listed by the CDC CVX codes (codes that indicate the product used in a vaccine) for tracking vaccination records. Huvax has provided cross-references based on these CDC CVX codes. Huvax provides ways for users to search, compare, and analyze licensed human vaccines. Various criteria can be used for querying human vaccines. Different vaccines can also be compared side by side. Vevax is a VIOLIN database of licensed veterinary vaccines (http //www. violinet.org/vevax). 

The UniProt KB is an automatically and manually annotated protein database drawn from translation of DDBJ/EMBL-Bank/GenBank coding sequences and directly sequenced proteins. Each sequence receives a imique, stable identifier allowing unambiguous identification of any protein across datasets. The KB also provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL-Bank/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain... 

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