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生物資訊程式語言應用 Part 7 Database Management by PHP. 2 Database Management and data presentation Database : MySqlMySql Tools : phpmyadminphpmyadmin Step 1 :

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Presentation on theme: "生物資訊程式語言應用 Part 7 Database Management by PHP. 2 Database Management and data presentation Database : MySqlMySql Tools : phpmyadminphpmyadmin Step 1 :"— Presentation transcript:

1 生物資訊程式語言應用 Part 7 Database Management by PHP

2 2 Database Management and data presentation Database : MySqlMySql Tools : phpmyadminphpmyadmin Step 1 : Creating a database and tables in MySql To create a database To create a table and to define attributes Insert data (By program-Perl or manual)Perl Step 2 : Develop a website for this database Selection / insertion / deletion / updating According to user requirements.

3 3 Flow Chart Perl PHP MySql

4 4 Management and presentation for PubMed data Management Selection Insertion Deletion Updating Link Files Index.php abstract.php abstractDel.php abstractUpd.php abstractUpdInt.php abstractIns.php abstractNew.php

5 5 Management and presentation for PubMed data Management Selection Insertion Deletion Updating Link Files Index.php abstract.php abstractDel.php abstractUpd.php abstractUpdInt.php abstractIns.php abstractNew.php

6 6 The query frame (index.php) SQL: SHOW COLUMNS FROM article FROM summer;

7 7 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

8 8 Selection (article.php) Select abstract and key in “interaction”. SELECT * FROM article where abstract like '%interaction%'

9 9 Selection (article.php) (con.)

10 10 Setup for DB link SQL Obtain records

11 11 Exercise article.php article_html.php article_php.php index.php index_html.php index_php.php To build article.php and index.php by *_php.php and *_html.php

12 IKM Manage database by Phpmyadmin. How do we manage the database by phpmyadmin? How do we manage the database by PHP?

13 13

14 14

15 15 UpdatingDeletiion Insertion

16 16 Insertion

17 17 Insertion (con.)

18 18 Updating

19 19 Deletion

20 20 Exercise Use 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.

21 21 Build a new frame for insertion, deletion and updating. (article.php)

22 22 Exercise Include insertion, updating, deletion buttons in article.php You may apply article_IDUtag.php to finish you practice.

23 23 Management and presentation for PubMed data Management Selection Insertion Deletion Updating Link Files Index.php abstract.php abstractDel.php abstractUpd.php abstractUpdInt.php abstractIns.php abstractNew.php

24 24 Insertion-Abstract Insert frame (article_new.php) Send two massages (pmid, year, title, abstract) to articleIns.php

25 25 Exercise articleNew.php What is the target file you want to send these massages?

26 26 Insertion - Insert into MySql (articleIns.php) Setup for DB link SQL Get massages

27 27 Exercise Please to finish insertion step by modifying articleIns.php.

28 28 Management and presentation for PubMed data Management Selection Insertion Deletion Updating Link Files Index.php abstract.php abstractDel.php abstractUpd.php abstractUpdInt.php abstractIns.php abstractNew.php

29 29 Updating (article.php)

30 30 Updating (articleUpd.php)

31 31 Exercise articleUpd.php articleUpd_php.php To build articleUpd.php and by articleUpd_php.php and articleUpd_php.php

32 32 Updating (con.) (articleUpdInt.php) Setup for DB link SQL

33 33 Exercise Please to finish Updating step by modifying articleUpdIns.php.

34 34 Management and presentation for PubMed data Management Selection Insertion Deletion Updating Link Files Index.php abstract.php abstractDel.php abstractUpd.php abstractUpdInt.php abstractIns.php abstractNew.php

35 35 Deletion (article.php)

36 36 Deletion (con.) (articleDel.php) Setup for DB link SQL

37 37 Exercise Please to finish Deletion step by modifying articleDel.php.

38 Extract sequences from the NCBI By user query http://www.ncbi.nlm.nih.gov/ By FTP ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/protein/prot ein.fa.gz ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/RNA/rna.fa. gz 38

39 Insert the sequences to database To construct the table for the sequences. To use the program to insert the sequences in the table. Perl code (practice) 39

40 40 Exercise Use 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.

41 41 Combine article.php and articleNew.php article.php?option=add

42 分頁 42

43 分頁 43

44 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 : 如果 start 是負數,傳回的字串將會從 string 結尾的第 start 個字開始。 44

45 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 : 45

46 Translate the nucleotide to amino acid $codons = substr ($sequence, $first, $first+2); 46

47 Submit a sequence to blast by the interface http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PRO GRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS= on&LINK_LOC=blasthome 47

48 Hyperlink for the sequence id http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term= Example: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=gi|19 4473734|ref|NM_181054.2| Homo sapiens hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) (HIF1A), transcript variant 2, mRNA 48

49 49 Resources MySql http://dev.MySql.com/http://dev.MySql.com/ Perl http://www.perl.com/http://www.perl.com/ phpmyadmin http://sourceforge.net/projects/phpmyadmin/ http://sourceforge.net/projects/phpmyadmin/ php http://www.php.net/http://www.php.net/


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