生物資訊程式語言應用生物資訊程式語言應用 Part 5Part 5

Perl and MySQL ApplicationsPerl and MySQL Applications

Outline Application one.

How to get related literature from PubMed? To store search results in database and find query

keyword.

Application two. How to establishment your own dictionary?

Application three. How to search detail information, like TF-TF relations

et al.

Application four. To construct co-occurrence graph.

Application one Keyword search.

Database

Keyword

Application one cont. Search results.

Application one cont. XML document.

Application one cont. Practice.

To get related literature that you want to known in XML data format by using PubMed web service in NCBI website. (like E2F1, ERE et al.)

Advanced exercise. To get sequence data from PubMed. To establish sequence database by using Perl and

MySQL.

Application one cont. Procedure.

MEDLINE Database

PubMed Web Service

Related Literatures

Application one cont. What Perl language need?

Some Perl packages. Known data (input data).

User query keyword, like “Estrogens”.

Information (output data). Query results, like “Estrogens related candidate data”.

Knowledge (related data). Data mining (extraction) from related candidate data.

Information KnowledgeData Sets

Application one cont.

Information

User Query

PubMed Online Database

Output File

User want to know

Download onlineService from PubMed

Candidate relatedLiteratures

Output file of XML data

Application one cont. Definition. Packages and input data.

Application one cont. Getting related literatures.

Application one cont. Results (XML file data)

Application one cont. Practice.

Using perl language to get related XML data.

Application one cont. To store search results.

XML File

MySQL Database

Data Analysis

Literature data (PMID, Year et.al)

XML format dataof query results

Data analysis forpreparing to store data

Query results inMySQL Database

Application one cont. To store search results.

Definition.

Application one cont. Storing search results.

Application one cont. MySQL data.

Application one cont. Practice.

To store obtained data into MySQL database. PMID Journal name Article Title Abstract PubDate

Application one cont. To find query keyword.

All Literatures

MySQL Database

Tagged ResultsWeb Page

Tagging

User Query

Query Keyword

Tagging keyword

All Literatures inMySQL Database

Tagging All LiteraturesAccording to Keyword

Displaying TaggedResults by Web Page

Application one cont. Definition.

Application one cont. Query keyword tagging.

Application one cont. Tagged results.

Application one cont. Practice.

Tagging related abstracts from candidate literatures. Gene name or protein name. Action words.

Application one cont. Challenge.

A tagging program that include two query words. Query word one.

Tagged abstracts. Un-tagged abstracts.

Query word two. Tagged abstracts. Un-tagged abstracts.

Complete data extraction system.

Get Related Literatures from PubMed

Store Related Literatures into Database

Find Some Information from Text File or Database

Application two To establish transcription factor (TF)

dictionary. From EBI-SRS online resource.

To get TF text data from EBI-SRS. Using Perl language to extract some data. To store data into MySQL by Perl language.

操作示範

Practice.

Application three To search TF-TF relations from established

literatures. Using TF dictionary. Using Perl language to extract co-occurrence

relations.

操作示範

Practice.

Application four To construct TF-TF co-occurrence graph.

Using Graphviz tools. http://www.graphviz.org/

TF-TF co-occurrence relations from established literatures.

操作示範

Practice.