SEARCH TEXT formation

Search for publications about piceol is documented in full text format in the CJACS file (Chemical Journals of the American Chemical Society) (Fig. 124). 

This section provides data on specific transcripts and proteins, including which protein is encoded by which transcript, transcript exon structure, protein domains, and subcellular localization. Expression pattern data (including Northern and Western blot data as well as in situ hybridization and antibody staining data) are presented both in a tabulated form using a controlled vocabulary format and in a detailed free-text format. An image-based expression pattern search tool, which can access data captured in the controlled vocabulary format, is being developed. 

SD structure file or a file containing a list of identification numbers [Excel or Comma Separated Value (CSV) format] can be uploaded. In the Excel or CSV cases the protocol will automatically look up the structure that corresponds to the identification number, as it does for the text box input. A useful feature (see Databases under Parameters in Fig. 7) is the ability to search multiple databases in a single search. This is made possible by the use of Perl in the Pipeline Pilot protocol. The Perl code is very general and easily allows for the addition of new databases as they become available, thereby further increasing the versatility of this protocol. 

Because formatting within an electronic resume is often minimal, what you say within your resume is what ultimately gets you hired. According to www.eresumes.com, "Keywords are the basis of the electronic search and retrieval process. They provide the context from which to search for a resume in a database, whether the database is a proprietary one that serves a specific purpose, or whether it is a web-based search engine that serves the general public. Keywords are a tool to browse quickly without having to access the complete text. Keywords are used to identify and retrieve resumes for the user. 

Each set of coordinates deposited with the PDB becomes a separate entry. Each entry is associated with an accession PDB code with a unique set of four alphanumeric characters. PDB and its mirror sites offer a text search engine that uses an index of all the textual information in each PDB record (e.g., PDB ID) an example of such an index is 1LYZ for hen s egg-white lysozyme. The first character is a version number. An identifier beginning with the number 0 signifies that the entry is purely bibliographic. The pdb file is a text file with an explanatory header followed by a set of atomic coordinates. The atomic coordinates are subjected to a set of standard stereochemical checks and are translated into a standard entry format for example, Figure 4.10 shows partial coordinate file for ILYZ.pdb or pdblLYZ.ent. 

The common atomic coordinate files for 3D structure in biochemistry is PDB format. The pdb files of polysaccharides, proteins, and nucleic acids can be retrieved from the Protein Data Bank at RCSB (http //www.rcsb.org/pdb/). On the home page (Figure 4.15), enter PDB ID (check the box query by PDB id only ) or keywords (check the box match exact word ) and click Find a structure button. Alternatively, initiate search/retrieval by selecting SearchLite. On the query page, enter the keyword (e.g., the name of ligand or biomacromolecule) and click Search button. Select the desired entry from the list of hits to access Summary information of the selected molecule. From the Summary information, select Download/Display file and then PDB Text and PDB noncompression format to retrieve the pdb file. In order to display 3D structure online, choose View structure followed by selecting one of 3D display options. The display can be saved in. jpg or. gif image format. 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

To facilitate the validation process on the basis of the above approach, the MS electronic data is contributed to the OPCW Laboratory in any of the following electronic formats JCAMP, NIST ASCII, AMDIS, and NIST MS Database. Contributing laboratories provide mostly the NIST MS Database format, with structures. The OPCW Code and the Schedule number are placed in the synonym field of the database. The file is submitted to the OPCW Laboratory either as the NIST MS User Database or the corresponding set of text files representing the MSP (Spectral) and MOL (Structure) information. The NIST MS Search/Analysis programs are used for the management of the MS electronic data and also GC(RI) once merged with the MS data. 

The use of computer-readable formats for chemical structures has become a compelling need to capture this information in databases or to simply annotate documents (Degtyarenko et al. 2007). Annotating full text documents with these machine-readable forms can make documents easier to search, and the intended structure can be visualized in context. The development of computer-readable formats started in earnest around 1990 (Borkent et al. 1988 Weininger 1988 Contreras et al. 1990 Ibison et al. 1993). 

Nowadays, thanks to the availability, cost, and ease-of use of chemical structure databases, many of these text databases have been converted into a structure format, and most chemical databases are now structure searchable. A simple search of the Internet will show that many databases still lack chemical structures and therefore are not searchable by structure in the original format, for example, an online HTML page. These pages, however, can contain valuable information and, with the application of the appropriate name-to-structure (N2S) conversion tools can be made searchable. 

The following subset dictionaries have been published in recent years from the Chapman Hall/ CRC database, and are intended as desktop references for the specialist worker. Now published by CRC Press each (except the older titles) consists of a large, single-volume printed dictionary accompanied by a fully searchable CD-ROM uniform in format and search capabilities (including substructure searching) with the main database. A new interface for text and structure searching by ChemAxon was released in 2009. 

The EPO esp cenet (ep.espacenet.com) database contains more than 60 million patents from 85 conntries worldwide (not just European Convention countries). The database is searchable by application number, assignee, inventor, or keywords from the title or abstract. Chemical structure searches are not possible. Patents can be viewed as images of the original document in PDF format one page at a time, or the whole patent can be viewed as a text document. Instantaneous translation from French or German into English is available for the latter document type if required. Equivalent pnblished patents, if any, are also listed and are available in PDF format. The text documents do not show chemical structures or diagrams, but these can be viewed in PDF format if required. 

Free patent information is provided by the website http //www.freepatentsonline.com/, covering U.S., EP, and PCT patents/applications and Japanese patent abstracts. In addition to the usual text-based searches in various search fields, this site also enables graphically input chemical structure searches to be performed on over 9 million compounds (including prophetic compounds) using exact structure, substructure, or chemical similarity searches. Chemistry searches using SMILES strings or chemical names are also possible. Full patent documents may be viewed in text or PDF format. 

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