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Primig lab [email protected] http://www.bioz.unibas.ch/primig Thomas Aust Roopa Basavaraj (visiting scientist) Michel Bellis (visiting scientist) Guenda Berthold Philippe Demougin Leandro Hermida Reinhold Koch Ulrich Schlecht Christa Wiederkehr Roland Zuest

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Primig lab

[email protected]

http://www.bioz.unibas.ch/primig

Thomas Aust

Roopa Basavaraj (visiting scientist)

Michel Bellis (visiting scientist)

Guenda Berthold

Philippe Demougin

Leandro Hermida

Reinhold Koch

Ulrich Schlecht

Christa Wiederkehr

Roland Zuest

Bioinformatics I -- Databases

Primig lab

[email protected]

http://www.bioz.unibas.ch/primig

Thomas Aust

Roopa Basavaraj (visiting scientist)

Michel Bellis (visiting scientist)

Guenda Berthold

Philippe Demougin

Leandro Hermida

Reinhold Koch

Ulrich Schlecht

Christa Wiederkehr

Roland Zuest


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Primig lab

[email protected]

http://www.bioz.unibas.ch/primig

Thomas Aust

Roopa Basavaraj (visiting scientist)

Michel Bellis (visiting scientist)

Guenda Berthold

Philippe Demougin

Leandro Hermida

Reinhold Koch

Ulrich Schlecht

Christa Wiederkehr

Roland Zuest

Microarray

Data

Bioinformatics I -- Databases

Primig lab

[email protected]

http://www.bioz.unibas.ch/primig

Thomas Aust

Roopa Basavaraj (visiting scientist)

Michel Bellis (visiting scientist)

Guenda Berthold

Philippe Demougin

Leandro Hermida

Reinhold Koch

Ulrich Schlecht

Christa Wiederkehr

Roland Zuest


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Schwede lab

[email protected]

http://www.bioz.unibas.ch/schwede

Jozef Aerts

Juergen Kopp

Flavio Monigatti

Franziska Roeder

Rainer Poehlmann

SWISS-MODEL

Protein

Database

Bioinformatics I -- Databases

Schwede lab

[email protected]

http://www.bioz.unibas.ch/schwede

Jozef Aerts

Juergen Kopp

Flavio Monigatti

Franziska Roeder

Rainer Poehlmann


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Bioinformatics I -- Databases

What is a database?

How do you make one?

Biological Databases

Knowledgebases

Novel ideas…

more Info at

http://www.biozentrum.unibas.ch/personal/primig/

Follow the >>>teaching<<< link.

What is a database?

How do you make one?

Biological Databases

Knowledgebases

Novel ideas…

more Info at

http://www.biozentrum.unibas.ch/personal/primig/

Follow the >>>teaching<<< link.

What is a database?

How do you make one?

Biological Databases

Knowledgebases

Novel ideas…

more Info at

http://www.biozentrum.unibas.ch/personal/primig/

Follow the >>>teaching<<< link.


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Bioinformatics I -- Databases

What is a database?

A database is a structured collection of data

Data INPUT >>> Information OUTPUT

Data INPUT >>> Information OUTPUT


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Bioinformatics I -- Databases

What is a relational database?

A relational database is a set of tables containing data belonging to defined categories

Data INPUT >>> Information OUTPUT


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Bioinformatics I -- Databases

How do you make one?

A relational database management system (RDBMS) lets you construct, update, and administrate a relational database. An RDBMS takes Structured Query Language (SQL) statements entered by a user and creates, updates, or provides access to the database.


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Bioinformatics I -- Databases

RDBMS

Open Source: mySQL | PostgreSQL

Commercial: IBM-DB2 | Oracle


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Bioinformatics I -- Databases

Accessing relational databases

You also need a Graphical User Interface (GUI).

PHP (recursive acronym for "PHP: Hypertext Preprocessor") is a widely-used Open Source general-purpose scripting language that is especially suited for Web development and can be embedded into HTML

Perl is derived mostly from the C programming language. Perl's process, file, and text manipulation facilities make it particularly well-suited for tasks involving e.g. database access, graphical programming, and world wide web programming.


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Bioinformatics I -- Databases

How do you make one?

  • Database Model:

  • Analyse aims (submission/curation system)

  • Define entities = tables (user, submission)

  • Define attributes (name, phone, email)

  • Define relationships between entities (user makes submission)

  • Draw diagram


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Bioinformatics I -- Databases

New

Assign

Submission

GeO

Curate

Submission

Author

Curator

Author

Author

Delete

Revision

Delete

Publication

Accepted

Rejected

Revise

GeO

GeO

Author

Curator

GeO

Curate

Revision

Assign

Revision

GeO

Deleted

GeO

GeO

Christa Wiederkehr


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Bioinformatics I -- Databases

How do you make one?

  • Database Model:

  • Analyse aims (submission/curation system)

  • Define entities = tables (user, submission)

  • Define attributes (name, phone, email)

  • Define relationships between entities (user makes submission)


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Orf

#orf_id

#nomenclature_id

#orf_name

Submitstate

#submitstate_id

*submitstate

Term

#term_id

*name

*term_type

Termassign

#go_acc

*submission_id

*ontology

User

#user_id

*name

*email

*login

*password

*lab_id

*user_role_id

Submission

#submission_id

*title

*description

°submitstate_id

°orf_id

*user_id

°curator_id

Reference

#reference_id

*title

*authors

*journal

*pubmed

°url_pdf

*submission_id

User_role

#user_role_id

*user_role

Comment

#comment_id

*text

*submission_id

*user_role_id

Bioinformatics I -- Databases

Christa Wiederkehr


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Bioinformatics I -- Databases

Biological Databases: DNA

DNA Sequence Data

EBI: http://www.ebi.ac.uk/

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

DDBJ:http://www.ddbj.nig.ac.jp/


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Bioinformatics I -- Databases

Global data synchronization


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Mouse

Rat

Human

Bioinformatics I -- Databases

EBI – EMBL

Release 72 contains 18,324,246 sequence entries

comprising 23,090,186,146 nucleotides


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Bioinformatics I -- Databases

Biological Databases: DNA

DNA Sequence Datasubmission at

http://www3.ebi.ac.uk/Services/webin/Sbm.cgi


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Bioinformatics I -- Databases

Biological Databases: proteins

Protein Structure Data

Protein Databank (PDB) at http://www.rcsb.org/pdb/

Search 17’107

Petide,

Protein and

Virus

Structures


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Bioinformatics I -- Databases

Biological Databases: proteins

Protein Structure Data Submission

at http://deposit.pdb.org/adit/


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Bioinformatics I -- Databases

Biological Databases: compounds

Small Molecules

Klotho DB: Biochemical Compounds Declarative Database at http://www.biocheminfo.org/klotho/

LIGAND DB at http://www.genome.ad.jp/kegg/catalog/compounds.html


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Bioinformatics I -- Databases

Biological Databases: RNA

  • Expression data - RNA

    • Microarray data repositories

    • GeneOmnibus (NCBI) at

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

    • ArrayExpress (EBI) at

    • http://www.ebi.ac.uk/arrayexpress/

    • MIAME:Minimal Information About a Microarray Experiment



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Bioinformatics I -- Databases

Biological Databases: RNA

  • Expression data - RNA

    • Expression data visualization

    • Stanford Expression Connection at

    • http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl

    • GermOnline at http://germonline.org

    • RIKEN mouse at http://read.gsc.riken.go.jp/



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Bioinformatics I -- Databases

Biological Databases: RNA

  • Expression data - RNA

    • Yeast Cell Cycle at http://genome-www.stanford.edu/cellcycle

    • Human Cell Cycle at http://genome-www.stanford.edu/Human-CellCyle/Hela

    • Human & Mouse tissue profiling at http://expression.gnf.org



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Bioinformatics I -- Databases

Biological Databases: proteins

  • Post-translational data: protein-protein interaction in Yeast

    • Biochemical studies

    • Cellzome

    • BIND

    • MDS Proteomics

    • Two-hybrid studies

    • Curagen’s PathCalling


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Bioinformatics I -- Databases

Biological Databases: proteins

  • Post-translational data: protein-protein interaction in Yeast

    • Biochemical studies

    • Cellzome at http://yeast.cellzome.com

    • BIND at http://bind.mshri.on.ca

    • MDS Proteomics at http://www.mdsp.com

    • Two-hybrid studies

    • Curagen’s PathCalling at http://portal.curagen.com

Access the data through http://germonline.bioz.unibas.ch and click on S. cerevisiae. Search for any gene, e.g. SPO11 and go to the Protein/Proteome Information section of the Locus Report page.



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Bioinformatics I -- Databases

Biological Databases: literature

Pubmed contains the abstracts of peer-reviewed publications in the field of biomedical research

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

Scientific Journals are often available online (sometimes even for free)!

http://www.ub.unibas.ch/vlib/vbbiol.htm


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Bioinformatics I -- Databases

Knowledgebases: a common language

The GeneOntology project: http://www.geneontology.org

The objective of GO is to provide controlled vocabularies for the description of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them.

The three organizing principles of GO are molecular function, biological process and cellular component. A gene product has one or more molecular functions and is used in one or more biological processes; it may be, or may be associated with, one or more cellular components.

The GeneOntology project: http://www.geneontology.org

The objective of GO is to provide controlled vocabularies for the description of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them.

The three organizing principles of GO are molecular function, biological process and cellular component. A gene product has one or more molecular functions and is used in one or more biological processes; it may be, or may be associated with, one or more cellular components.


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Bioinformatics I -- Databases

Knowledgebases: a common language

  • The GeneOntology Evidence Code:http://www.geneontology.org/doc/GO.evidence.html

  • IC inferred by curator (no evidence but reasonable)

  • IDA inferred from direct assay (enzyme, EMSA)

  • IEA inferred from electronic annotation (BLAST hit)

  • IEP inferred from expression pattern (RNA, Protein)

  • IGI inferred from genetic interaction (suppressors, synthetic lethals, complementation)

  • IMP inferred from mutant phenotype (deletion, insertion)

  • IPI inferred from physical interaction (co-IP, 2-hybrid)

  • ISS inferred from sequence or structural similarity (homolog)

  • NAS non-traceable author statement (quote cannot be found)

  • ND no biological data available

  • TAS traceable author statement

  • NR not recorded


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Bioinformatics I -- Databases

Biological Databases: GO based species specific db’s

  • Annotation: covers knowledge from Genetics, Molecular Biology and Functional genomis

  • SGD for S. cerevisiae

    • http://genome-www.stanford.edu/Saccharomyces/

  • TAIR for A. thaliana

    • http://www.arabidopsis.org/

    • Wormbase for C. elegans

    • http://www.wormbase.org

    • Flybase for D. melanogaster

    • http://flybase.bio.indiana.edu/

    • Mouse Genome Database for M. musculus

    • http://www.informatics.jax.org


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Bioinformatics I -- Databases

Knowledgebases: Swissprot >>> Uniprot

Release 40.31 of 25-Oct-2002 of SWISS-PROT contains 116776 sequence entries, comprising 42881496 amino acids abstracted from 100002 references.


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Bioinformatics I -- Databases

Knowledgebases: Swissprot >>> Uniprot

  • KEY FEATURES

  • Minimal redundancy: data from different sources are merged; if conflicts exist between various sequencing reports, they are indicated in the feature table of the corresponding entry.

  • Annotation:

    • Function(s) of the protein

    • Post-translational modification(s). For example carbohydrates, phosphorylation, acetylation, GPI-anchor, etc.

    • Domains and sites. For example calcium binding regions, ATP-binding sites, zinc fingers, homeobox, kringle, etc.

    • Secondary structure

    • Quaternary structure. For example homodimer, heterotrimer, etc.

    • Similarities to other proteins

    • Disease(s) associated with deficiencie(s) in the protein

    • Sequence conflicts, variants, etc.

  • Integration

  • Swissprot is currently links to about 60 external databases (list at http://www.expasy.org/cgi-bin/lists?dbxref.txt)


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Bioinformatics I -- Databases

Knowledgebases: Swissprot >>> Uniprot

In SWISS-PROT, information is given in the comment lines (CC), in the feature table (FT) and in the keyword lines (KW). Most comments are classified by `topics'; this approach permits the easy retrieval of specific categories of data from the database.

ID SP11_YEAST STANDARD; PRT; 398 AA.

AC P23179;

CC -!- FUNCTION: REQUIRED FOR MEIOTIC RECOMBINATION. MEDIATES DNA CC CLEAVAGE THAT FORMS THE DOUBLE-STRAND BREAKS (DSB) THAT INITIATE CC MEIOTIC RECOMBINATION.

CC -!- SUBCELLULAR LOCATION: Nuclear.

CC -!- DEVELOPMENTAL STAGE: MEIOSIS-SPECIFIC.

CC -!- SIMILARITY: BELONGS TO THE TOP6A FAMILY.

FT ACT_SITE 135 135 DNA CLEAVAGE (PROBABLE).

FT MUTAGEN 135 135 Y->F: LOSS OF ACTIVITY.

KW Hydrolase; DNA-binding; Sporulation; Meiosis; Nuclear protein.


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Bioinformatics I -- Databases

Novel ideas…

A database that contains large-scale automatic structure predicitons: SWISS-MODEL repository

Models from SWISS-MODEL server and non-curated external sources will be available.


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Bioinformatics I -- Databases

Novel ideas…

The SWISS-MODEL server at http://www.expasy.org/swissmod/

is an automated modelling system that serves all scientist as a tool to study the putative 3D structure of a protein using Comparative Modelling.


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Bioinformatics I -- Databases

Novel ideas…

The GermOnline server at

http://germonline.bioz.unibas.ch

http://germonline.org

is a platform for online submission/curation that enables scientist who work in the field of meiosis and gametogenesis to create, update and curate a knowledgebase that uses controlled vocabulary (GO) and free text to describe the roles of genes in sexual reproduction.


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Bioinformatics I -- Databases

Major DB info EBI:

http://www.ebi.ac.uk/Databases

Nucl. Acid Res. 2002

http://nar.oupjournals.org/content/vol30/issue1/

GermOnline

http://germonline.unibas.ch

Primig lab

http://www.bioz.unibas.ch/personal/primig/

follow the teaching link, check out literature & info, download ppt presentation db’s.

Life Sciences Training Facility

http://www.bioz.unibas.ch/corelab: you will find more links on bioinformatics


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Bioinformatics I -- Projects

We would like to collaborate with you on our ongoing GermOnline project.

You will be asked to use online sources (species-specific and general knowledgebases, Pubmed) to collect information about the genomes of S. pombe, A. thaliana, C. elegans, D. melanogaster, M. musculus and H. sapiens. This information should be presented in a concise paragraph like the one written by Peter Philippsen for the genome of S. cerevisiae (click on S. cerevisiae and follow the more link in the Genome Information section). You should include two complete references. Furthermore we ask you to search for knowledge about a list of conserved genes important for meiosis and gametogenesis. You are asked to identify the homologs and orthologues and provide curated information about the yeast genes DMC1, MLH3, MRE11, MSH4, MSH5andSPO11. Your search should include literature, knowledgebases and protein structures. More info at

http://www.biozentrum.unibas.ch/personal/primig/teaching/bioinfo_I_literature.html

The information you provide will be integrated into GermOnline by Ulrich Schlecht. You will be credited for your contribution. The results you produce will be recorded and (if everything works out) they count for the exam. We look forward to getting your feedback.


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