1 / 12

Introduction to Practical 1 Biological databases

Introduction to Practical 1 Biological databases. Overview of L1. BIOINFORMATICS ~ biology + computers Data (databases) Query and Analysis of Data (software/tools) …. more on this in your upcoming lectures…. Biological databases. Structured storage of many kinds of data, including:

ora-hudson
Download Presentation

Introduction to Practical 1 Biological databases

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Introduction to Practical 1 Biological databases

  2. Overview of L1 BIOINFORMATICS ~ biology + computers • Data (databases) • Query and Analysis of Data (software/tools) ….more on this in your upcoming lectures….

  3. Biological databases • Structured storage of many kinds of data, including: • Sequence (eg chromosomal DNA, mRNA, protein) • Structures • Literature (eg PubMed) • Diseases • Biomolecular interactions • Etc etc etc etc

  4. Databases, continued: • Databases can come and go. • There can be: • Multiple databases for a single kind of data (eg protein sequence, pathways, etc) • New databases for “new” kinds of data • Every database has its own peculiarities And so….

  5. A good biologist • Acquires a general set of skills for FINDING and USING databases • “poke around” • “look” • “think” • Can critically assess the quality of a search (in terms of specificity, true positives (relevant hits) and false positives (irrelevant hits), as well as the contents of databases

  6. P1: a gentle introduction to databases LEARNING GOALS: • Know how to perform simple queries of several databases • Gain some familiarity with the contents of selected databases • Learn to identify distinct elements of database records • Use database cross references to link to other databases • Know multiple approaches to find biological data on the internet

  7. The exercise Section A) Take an introductory look at selected databases Section B) Find additional databases using the Nucleic Acids Research Database Issue

  8. Section A: An introductory look at biological databases Follow the instructions in the exercise to look at: • Protein: database of protein sequences • Gene: Whole genome annotation • OMIM: genes and diseases • KEGG Pathway: metabolic and signalling pathways • PDB: three-dimensional biomolecular structures

  9. Section B: the Nucleic Acids Research database issue – identifying useful databases • Hundreds of DBs out there, and more coming all the time • Various ways to find them:  Google etc  PubMed (eg p53 database)  Catalogs of the databases

  10. An example of a database catalogue: Nucleic Acids Research Database Issue • Special supplementary issue of the Nucleic Acids Research journal • Collection of all DBs published in NAR & selected DBs relevant to biologists • not complete, but contains most of the popular DBs • Hotlinks & brief summaries provided for each DB • Catalog List: Categorize the DBs based on different type of info • eg, sequence, structure, signaling, plant, metabolics, disease From: http://nar.oxfordjournals.org/content/39/suppl_1/D1/suppl/DC1

  11. Capture your answers Eg: • Capture your answers electronically by writing them in the exercise Ms Word document provide for each practical  Start a new Word document or Excel document… You work will be discussed before the end of the practical

  12. Begin your exercise work now

More Related