BioXing™

                                                                                                Solutions for Biotechnology

Home Up Search Feedback

Infrastructure
Infrastructure Lab WorkFlow Instrument Workflow Distributed Architecture

 

 

 

This figure shows the relationship between a Web Service, different types of data storage, Web and Client applications and other Web services. In this model a Web Service contains a collection of Data Readers and Data Writers for reading and writing of disparate types of data in different storage formats.  Examples of disparate types of data are arrays of data from microarrays and spectral analyzers, gel images,  pictures, sequences,  annotations, protocols and journal articles.  Applications access  the data and information through a common API (Application Programming Interface) that binds the appropriate reader and writer. That is, a Web Service behaves similarly to a computer operating system which uses device drivers to access disparate hardware devices.  In addition, Web Services can provide standard components that contain algorithms for analysis, filtering, correlating and integration.  An important advantage of a Web Service is that when a component is updated or when new components are added then all applications benefit.  Since Web Services can be linked to other Web Services and since applications can use multiple Web Services; Web Services can be constructed for specific functionality such as a Web Service could be dedicated to DNA Microarrays, to Protein arrays, to Mass Spectral data, to genomic databases or to  proteomic databases.

A Web Service can have public and private programming interfaces to enable or restrict access to specific functionality for applications across the internet and intranet. For example, it is possible to design a web page that displays information retrieved by utilizing API from multiple web services.

Data can be stored in a variety of formats such as relational databases that are local or distributed across a network, Text files or Binary files. Text files have a variety of formats including keyword based such as GenBank and SwissProt, XML tag structured, fixed column and other structures (e.g. Fasta format, CSV (Character Separated Variables such as commas and tabs) )  where all files can be viewed using a standard text editor. Binary files are usually proprietary formatted files (e.g. Mass Spectrums, Images, pictures, ...)  and can only be viewed with applications that have knowledge of their format.  Web Services may provide the capability of reading Text and Binary files to transfer the content to relational databases where the standard database query language (SQL) can be used for further accessing and integration with other content.

The following table provides examples of different types of Text files being used in bioinformatics. Documents are available that describe their format and content.

Keyword based text files Swiss-Prot entry:

Each line has a two character code followed by a space and then the content of the line which has a well defined format structure. The only exception is the actual sequence. 

ID 104K_THEPA STANDARD; PRT; 924 AA.
AC P15711;
DT 01-APR-1990 (REL. 14, CREATED)
DT 01-APR-1990 (REL. 14, LAST SEQUENCE UPDATE)
DT 01-AUG-1992 (REL. 23, LAST ANNOTATION UPDATE)
DE 104 KD MICRONEME-RHOPTRY ANTIGEN.
OS THEILERIA PARVA.
OC EUKARYOTA; ALVEOLATA; APICOMPLEXA; PIROPLASMIDA; THEILERIIDAE;
OC THEILERIA.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=MUGUGA;
RX MEDLINE; 90158697.
RA IAMS K.P., YOUNG J.R., NENE V., DESAI J., WEBSTER P.,
RA OLE-MOIYOI O.K., MUSOKE A.J.;
RT "Characterisation of the gene encoding a 104-kilodalton microneme-
RT rhoptry protein of Theileria parva.";
RL MOL. BIOCHEM. PARASITOL. 39:47-60(1990).
CC -!- SUBCELLULAR LOCATION: IN MICRONEME/RHOPTRY COMPLEXES.
CC -!- DEVELOPMENTAL STAGE: SPOROZOITE ANTIGEN.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; M29954; G161866; -.
DR PIR; A44945; A44945.
KW ANTIGEN; SPOROZOITE; REPEAT.
FT DOMAIN 1 19 HYDROPHOBIC.
FT DOMAIN 905 924 HYDROPHOBIC.
SQ SEQUENCE 924 AA; 103625 MW; 4563AAA0 CRC32;
MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL
QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG
DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN
GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK
YVPISQKNYE TGIVKLKDYK HAYHPVDLDI KDIDYTMFHL ADATYHEPCF KIIPNTGFCI
TKLFDGDQVL YESFNPLIHC INEVHIYDRN NGSIICLHLN YSPPSYKAYL VLKDTGWEAT
THPLLEEKIE ELQDQRACEL DVNFISDKDL YVAALTNADL NYTMVTPRPH RDVIRVSDGS
EVLWYYEGLD NFLVCAWIYV SDGVASLVHL RIKDRIPANN DIYVLKGDLY WTRITKIQFT
QEIKRLVKKS KKKLAPITEE DSDKHDEPPE GPGASGLPPK APGDKEGSEG HKGPSKGSDS
SKEGKKPGSG KKPGPAREHK PSKIPTLSKK PSGPKDPKHP RDPKEPRKSK SPRTASPTRR
PSPKLPQLSK LPKSTSPRSP PPPTRPSSPE RPEGTKIIKT SKPPSPKPPF DPSFKEKFYD
DYSKAASRSK ETKTTVVLDE SFESILKETL PETPGTPFTT PRPVPPKRPR TPESPFEPPK
DPDSPSTSPS EFFTPPESKR TRFHETPADT PLPDVTAELF KEPDVTAETK SPDEAMKRPR
SPSEYEDTSP GDYPSLPMKR HRLERLRLTT TEMETDPGRM AKDASGKPVK LKRSKSFDDL
TTVELAPEPK ASRIVVDDEG TEADDEETHP PEERQKTEVR RRRPPKKPSK SPRPSKPKKP
KKPDSAYIPS ILAILVVSLI VGIL
//

XML Beginning and Ending Tags are paired angular bracketed names with a format of:

<name>...</name>

Data contained between beginning and ending tags can be text, numbers, images and blobs (Binary Large Objects)

 <Elements>
<AtomicNbr>1</AtomicNbr>
<Element>Hydrogen</Element>
<Symbol>H</Symbol>
</Elements>
<Elements>
<AtomicNbr>2</AtomicNbr>
<Element>Helium</Element>
<Symbol>He</Symbol>
</Elements>
<Elements>
<AtomicNbr>3</AtomicNbr>
<Element>Lithium</Element>
<Symbol>Li</Symbol>
</Elements>
<Elements>
<AtomicNbr>4</AtomicNbr>
<Element>Beryllium</Element>
<Symbol>Be</Symbol>
</Elements>
<Elements>
<AtomicNbr>5</AtomicNbr>
<Element>Boron</Element>
<Symbol>B</Symbol>
</Elements>

...
Fixed Column 4 fixed width columns with defined data in each column AAV2  V 010804: N=Adeno-associated virus 2
                C=AAV2
ABIMA E 003320: N=Abies magnifica
                C=Red fir
ABMVW V 010816: N=Abutilon mosaic virus (isolate West India)
ABRPR E 003816: N=Abrus precatorius
                C=Indian licorice
                S=Crab's eye
ABSGL E 004829: N=Absidia glauca
                C=Pin mould
ABUPI E 008989: N=Aburria pipile
                C=Common piping guan
                S=Trinidad piping guan
ABUTH E 003631: N=Abutilon theophrasti
                C=China jute
                S=Indian mallow

Other

FASTA - line 1 is a header with defined notation and vertical bars separating data fields. Lines 2 to N contain the sequence with a maximum line length.

 

>sp|P21589|5NTD|5'-NUCLEOTIDASE PRECURSOR (EC 3.1.3.5) (ECTO-NUCLEOTIDASE) (5'-NT) (CD73 ANTIGEN).
MCPRAARAPATLLLALGAVLWPAAGAWELTILHTNDVHSRLEQTSEDSSKCVNASRCMGGVARLFTKVQQIRRAEPNVLL
LDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVEGLIEPLLKEAKFPILSANIKAKGPLASQISGLYLP
YKVLPVGDEVVGIVGYTSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEMDKLIAQKVRGVDVVV
GGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKVPVVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLNSSIPEDPSI
KADINKWRIKLDNYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRHTDEMFWNHVSMCILNGGGIRSPIDE
RNNGTITWENLAAVLPFGGTFDLVQLKGSTLKKAFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVLCTKCR
VPSYDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDINVVSTYISKMKVIYPAVEGRIKFSTGSHCHGSFSL
IFLSLWAVIFVLYQ

NetFormatics and BxNetRef are collections of products that are client based and provide for viewing, analyzing and managing data through the Web Services.

WebFormatics and BxWebRef are collections of products that are Web based and provide for viewing, analyzing and managing data through the same Web Services.

 

 

Home ] Up ]

Send mail to info@BioXing.com with questions, comments or requests for information.
Copyright © 1999-2017 BioXing. All rights reserved. Use or reproduction without authorization from BioXing is strictly prohibited. By using this site you accept its Terms and Conditions.
Last modified: May 2017