BioInfoBase Data Entry Instruction

 

* The main fields for the current version of the website are highlighted.

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Timestamp: Date and time of the record registration (automatically inserted).

Original Code: The record code provided by the admin. If you are the “Record Creator” you may use your own code.

e.g.      G-S-SM-719

Record Creator: Name of the person who provided you with this record.

e.g.      Admin

Record Registrar: Name of the person completing the record.

e.g.      Dana Dereeper

Record Maintainer: Name of the person who verifies and maintains the record.

e.g.      Dana Dereeper

Name: Record name as the following format;

Acronym of the record (if any): Full name of the record

e.g.      - REDfly: Regulatory Element Database for Drosophila

                        - Signal-3L: A 3-layer approach for predicting signal peptides

                        - ImageJ

First Category: Select the main category to which the record belongs.

e.g.      Database

Second Category: Select one or more subcategories to which the above main category belongs.

e.g.      Genomics

Application: The general use of the record. Not more than 100 characters (with space).

e.g.      - Predicting subcellular localization

                        - Molecular dynamics simulation

                        - Image processing and analysis in Java

Organism Common Name: Common name of the organism(s) which the record focuses on.

e.g.      - Rice

            - Mammalian

Organism Scientific Name: Scientific name of the organism(s) which the record focuses on.

e.g.      Oryza sativa

Authors/Developers: Name of the person(s) who developed the software/database/…

e.g.      Kuo-Chen Chou, Gautam B. Singh, Hong-Bin Shen

Keywords: Major keywords (3-6) related to the record as could be found in relevant article, if any, else, extract from the record’s main theme.

e.g.      EST, expression, regulatory elements, rice, RT-PCR

Features: Detailed information about the applications of the record. This is an important field for both the BioInfoBase search engine and the users.

e.g.      BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by a graduate student who knows how frustrating and time consuming it can be to rely upon word-processors and command-line programs for sequence manipulation. BioEdit is intended to supply a single program that can handle most simple sequence and alignment editing and manipulation functions that researchers are likely to do on a daily basis, as well as a few basic sequences analyses.

BioEdit offers a variety of useful features:

·         Four modes of manual alignment: select and slide, dynamic grab and drag, gap insert and delete by mouse click, and on-screen typing which behaves like a text editor.

·             In-color alignment and editing with separate nucleic acid and amino acid color tables and full control over background colors.

·             Plasmid drawing interface for automated creation of plasmid vector graphic from a DNA sequence.  Easily mark positions, add features with arrows and curved boxes, and mark restriction enzyme cut sites.  Also show detail of polylinker and draw moveable arrows and shapes with drawing tools.

·             Dynamic information-based alignment shading.

·             Point-and-click color table editing.

·             Display and print ABI chromatograms with ……

Platform: Accessibility to the record (online/offline/both).

e.g.      Online

Operating System: System compatibility of the record.

e.g.      Windows

Other System Requirements:

e.g       ·  512 MB RAM required

·  2 GB RAM recommended

·  1024 x 768 display recommended

·  32 and 64 bit platforms supported

·  Intel or AMD CPU required

Programming Language: The programming language used to develop the record.

e.g.      Python

License: Availability of the record as free or commercial.

e.g.      Free

Price: Price of the facilities provided by the record.

e.g.      1500 USD

Version: Updated version of the record.

e.g.      6.0.5

Abstract: Abstract of the relevant article, if any.

e.g.      PLACE is a database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. In addition to the motifs originally reported, their variations in other genes or in other plant species in later reports are also compiled. Documents for each motif in the PLACE database contains, in addition to a motif sequence, a brief definition and description of each motif, and relevant literature with PubMed ID numbers and GenBank accession numbers where available. Users can search their query sequences for cis-elements using the Signal Scan program at our web site. The results will be reported in one of the three forms. Clicking the PLACE accession numbers in the result report will open the pertinent motif document. Clicking the PubMed or GenBank accession number in the document will allow users to access to these databases, and to read the abstract of the literature or the annotation in the DNA database. This report summarizes the present status of this database and available tools.

Publication Citation: Citation of the relevant article (first and last version) according to NAR (Nucleic Acids Research) style.

e.g.      Dong,X., Stothard,P., Forsythe,I.J. and Wishart,D.S. (2004) PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res., 32, W660–W664.

Journal: The journal that published the relevant article, if any.

e.g.      Nucleic Acids Research

Journal Impact Factor (IF): Impact factor of the journal that published the article under citation, if any. You may use the following link to find the IF of the journal: http://www.bioxbio.com/if/

e.g.      8.278

Publisher: Name of the publisher to which the journal belongs, if any.

e.g.     Oxford University Press (OUP)

Google Scholar Citations: The number of citations of the relevant article given by Google Scholar, if any.

e.g.      Cited by 934

Web Link: The link of record’s home page.

e.g.      http://www.dna.affrc.go.jp/PLACE/index.html

Contact Information: Postal address of the record’s developer, if any.

e.g.      Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan

Email: Email address of the record developer.

e.g.      zuker@ibc.wustl.edu

Institution: Name of the institute where the record was developed.

e.g.      Institute for Biomedical Computing, Washington University

Country: Name the country where the institute is located.

e.g.      USA

User ranking: Usefulness of the record (ranking from 1-5) based on the registrar’s experience.

e.g.      3

Submit Review: Advantage or disadvantage of the record based on the registrar’s experience.

e.g.      MacVector is a comprehensive application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions. MacVector is often cited as the most intuitive, easy to use program available for sequence analysis and is championed by Mac users. It is not cross platform and this is its biggest drawback.

Download Related Manual: Please download the record manual, if accessible.

Download Related Paper: Please download the record article, if accessible.

Download Last Released Software Database: Please download updated version of the record (software/database/app), if accessible.

Tutorial: Web link for the record tutorials/webinars, if any.

e.g.      http://geneious.com/tutorials

Article Link: Web link for the record article, if any.

e.g.      http://david.abcc.ncifcrf.gov/forum/viewtopic.php?f=10&t=796

Miscellaneous: Any additional information you may extract from the record.

Ready for Publish:

Editing- if you couldn’t finish the record submission and need more time put it in “Editing” status.

Ready for publish- use this status if the record is ready for publish, so the admin will be prompted for verification and finalizing the submission. The record will then be analysed and provided to the search engine.

 

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