生物資訊程式語言應用 Part 7

生物資訊程式語言應用生物資訊程式語言應用Part 7Part 7

Database Management by PHPDatabase Management by PHP

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Database Management and data presentation

Database : MySql

Tools : phpmyadmin

Step 1 : Creating a database and tables in MySqlTo create a database

To create a table and to define attributes

Insert data (By program-Perl or manual)

Step 2 : Develop a website for this databaseSelection / insertion / deletion / updating

According to user requirements.

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Flow Chart

PubmedCrawl Pubmed

literatures/sequences by query keyword

Insertion Deletion

Updating

Database mmanagement and data presentation

User query Html

User query

Mark query term

Html

Selection

Perl

PHP

MySql

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Management and presentation for PubMed data

abstract.php

abstractNew.php abstractIns.php

abstractUpd.php abstractUpdIns.php

abstractDel.php

index.php

Insertion Deletion

Updating


User query

Html

Selection

ManagementSelection

Insertion

Deletion

Updating

Link

FilesIndex.php

abstract.php

abstractDel.php

abstractUpd.php

abstractUpdInt.php

abstractIns.php

abstractNew.php

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Management and presentation for PubMed dataManagement

SelectionInsertion

Deletion

Updating

Link

abstract.php



abstractDel.php

index.php

Files

Index.php

abstract.phpabstractDel.php

abstractUpd.php

abstractUpdInt.php

abstractIns.php

abstractNew.php

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The query frame (index.php)

SQL:SHOW COLUMNS FROM article FROM summer;

Selection

output

Input

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The query frame (index.php)

Send two massages (choice, text_query) to article.php

Example : To select abstract and key in “interaction”.

Setup for DB link

SQL

Obtain records

Selection

output

Input

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Selection (article.php)Select abstract and key in “interaction”.

SELECT * FROM article where abstract like '%interaction%'

Selection

output

Input

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Selection (article.php) (con.)

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Setup for DB link

SQL

Obtain records

Insertion Deletion

Updating


User query

Html

Selection

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Exercisearticle.php

article_html.php

article_php.php

index.phpindex_html.php

index_php.php

To build article.php and index.php by *_php.php and *_html.php

II KK MM

Manage database by Phpmyadmin.

How do we manage the database by phpmyadmin?

How do we manage the database by PHP?

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Updating Deletiion

Insertion

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Insertion

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Insertion (con.)

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Updating

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Deletion

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ExerciseUse phpmyadmin to insert a record to article table, and write down their executing SQL.

Use phpmyadmin to update a record to article table, and write down their executing SQL.

Use phpmyadmin to delete a record to article table, and write down their executing SQL.

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Build a new frame for insertion, deletion and updating. (article.php)

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ExerciseInclude insertion, updating, deletion buttons in article.php

You may apply article_IDUtag.php to finish you practice.

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Selection

InsertionDeletion

Updating

Link

abstract.php



abstractDel.php

index.php

FilesIndex.php


abstractUpd.php

abstractUpdInt.php

abstractIns.php

abstractNew.php

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Insertion-Abstract Insert frame (article_new.php)

Send two massages (pmid, year, title, abstract)

to articleIns.php

Abstract Insert frame

Insert into mysql

Insertion SQL

Input

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ExercisearticleNew.php

<FORM action="" name="" method="post">

What is the target file you want to send these massages?

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Insertion - Insert into MySql (articleIns.php)

Abstract Insert frame

Insert into mysql

Insertion SQL

Input

Setup for DB link

SQLGet massages

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ExercisePlease to finish insertion step by modifying articleIns.php.

abstract.php



abstractDel.php

index.php

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Selection

Insertion

Deletion

UpdatingLink

abstract.php



abstractDel.php

index.php

FilesIndex.php


abstractUpd.php

abstractUpdInt.phpabstractIns.php

abstractNew.php

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Updating (article.php)

Selection frame

Update the record

Selection SQL

Selected Information

Updating SQL

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Updating (articleUpd.php)

Selection frame

Update the record

Selection SQL


Updating SQL

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ExercisearticleUpd.php

articleUpd_php.php

articleUpd_php.php

To build articleUpd.php and by articleUpd_php.php and articleUpd_php.php

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Updating (con.) (articleUpdInt.php)

Selection frame

Update the record

Selection SQL


Updating SQL

Setup for DB link

SQL

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ExercisePlease to finish Updating step by modifying articleUpdIns.php.

abstract.php



abstractDel.php

index.php

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Selection

Insertion

DeletionUpdating

Link

abstract.php



abstractDel.php

index.php

FilesIndex.php

abstract.php

abstractDel.phpabstractUpd.php

abstractUpdInt.php

abstractIns.php

abstractNew.php

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Deletion (article.php)

Selection frame

Delete the record

Deletion SQL

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Deletion (con.) (articleDel.php)

Setup for DB link

SQL

Selection frame

Delete the record

Deletion SQL

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ExercisePlease to finish Deletion step by modifying articleDel.php.

abstract.php



abstractDel.php

index.php

Extract sequences from the NCBIBy user query

http://www.ncbi.nlm.nih.gov/

By FTPftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/protein/protein.fa.gz

ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/RNA/rna.fa.gz

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Insert the sequences to databaseTo construct the table for the sequences.

To use the program to insert the sequences in the table.

Perl code (practice)

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ExerciseUse phpmyadmin to select , insert , update, delete a record to sequence table, and write down their executing SQL.

Modified the article%.php for the sequences table.

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Combine article.php and articleNew.php article.php?option=add

分頁

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分頁

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To calculate particular information for sequences

Frequency語法 : string substr (string string, int start [, int length])

說明 : substr( ) 傳回 string 的一部份字串，由參數 start 和 length 指定。如果 start 是正數，傳回的字串將會從 string 的第 start 個字元開始。Example :

<?php

$rest = substr ("abcdef", 1); // returns "bcdef"

$rest = substr ("abcdef", 1, 3); // returns "bcd"

?>

如果 start 是負數，傳回的字串將會從 string 結尾的第 start 個字開始。

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To calculate particular information for sequences

CG%

Length語法 : int strlen (string str)

說明 : 傳回字串 str 的長度。

Example :

<?php

$DNA_length=strlen($a);

?>

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Translate the nucleotide to amino acid$codons = substr ($sequence, $first, $first+2);

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Submit a sequence to blast by the interfacehttp://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome

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Hyperlink for the sequence idhttp://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=

Example:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=gi|194473734|ref|NM_181054.2| Homo sapiens hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) (HIF1A), transcript variant 2, mRNA

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ResourcesMySql http://dev.MySql.com/

Perl http://www.perl.com/

phpmyadmin http://sourceforge.net/projects/phpmyadmin/

php http://www.php.net/

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生物資訊程式語言應用 Part 7