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Guest Lecture Graduate level course MCB221b - Mechanistic Enzymology Metabolic Networks Tobias Kind March 2010

2. Databases very short primer (*). Database interface is what you seeDatabase queries what you ask the databaseDatabase objects where the data is stored (index and tables)Database types relational databases, object oriented databases, flat file DBsDatabase brands Oracle, MySQL,

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Guest Lecture Graduate level course MCB221b - Mechanistic Enzymology Metabolic Networks Tobias Kind March 2010

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    1. 1 http://fiehnlab.ucdavis.edu/teaching/ CLICK on Slide SHOW – all documents and TOOLS are hyperlinked – IF the little hand is visible (or green text) please click to open in FireFox web browser (AGAIN, this only works with slideshow ON) ------- graduate level course Bainer Hall 1062   TTh 1:40-3:00 p.m. http://fiehnlab.ucdavis.edu/teaching/ CLICK on Slide SHOW – all documents and TOOLS are hyperlinked – IF the little hand is visible (or green text) please click to open in FireFox web browser (AGAIN, this only works with slideshow ON) ------- graduate level course Bainer Hall 1062   TTh 1:40-3:00 p.m.

    2. 2 Ontologies "ensure data integrity and logical consistency” Semantics – capture the meaning http://books.google.com/books?id=CHhc1BW0XKIC Semantics in Databases  By Bernhard Thalheim, Leonid LibkinOntologies "ensure data integrity and logical consistency” Semantics – capture the meaning http://books.google.com/books?id=CHhc1BW0XKIC Semantics in Databases  By Bernhard Thalheim, Leonid Libkin

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    4. 4 alc bgf bin box bs c3d1 c3d2 caccrt cache cacint car ccc cht cml crk2d crk3d csr cssr ct dmol ent,pdb feat fh fix,smi gam, gamout gamin,inp gau gcart gpr gr96a gr96n hin ins,res jin jout mdl mdl,mol mm1gp mmads mmd,mmod mmod,dat,mmd mol mol2 mopcrt mopout mpqc nw nwo out,dat pov pqs prep qcin qcout qm1gp report sd,sdf smi txyz unixyz vmol xyz alc bgf bin box bs c3d1 c3d2 caccrt cache cacint car ccc cht cml crk2d crk3d csr cssr ct dmol ent,pdb feat fh fix,smi gam, gamout gamin,inp gau gcart gpr gr96a gr96n hin ins,res jin jout mdl mdl,mol mm1gp mmads mmd,mmod mmod,dat,mmd mol mol2 mopcrt mopout mpqc nw nwo out,dat pov pqs prep qcin qcout qm1gp report sd,sdf smi txyz unixyz vmol xyz

    5. 5 SMARTS - Smiles ARbitrary Target Specification (for substucture searching) SMIRKS - SMARTS - Smiles ARbitrary Target Specification (for substucture searching) SMIRKS -

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    7. 7 http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html OpenSmiles may solve some problems, Good Canonizer needed. http://wwmm.ch.cam.ac.uk/inchifaq/http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html OpenSmiles may solve some problems, Good Canonizer needed. http://wwmm.ch.cam.ac.uk/inchifaq/

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    9. 9 InChI=1/C2H4ClNO2/c3-1(4)2(5)6/h1H,4H2,(H,5,6)/p+1/t1-/m1/s1/i3+0/fC2H5ClNO2/h4-5H/q+1 InChIKey: UWPWWENWLZPQGU-CQNODWLUHWInChI=1/C2H4ClNO2/c3-1(4)2(5)6/h1H,4H2,(H,5,6)/p+1/t1-/m1/s1/i3+0/fC2H5ClNO2/h4-5H/q+1 InChIKey: UWPWWENWLZPQGU-CQNODWLUHW

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    11. 11 Define standards (for curation) Define vocabulary Provide data repository for models Define standards (for curation) Define vocabulary Provide data repository for models

    12. 12 RDF - http://en.wikipedia.org/wiki/Resource_Description_Framework http://www2007.org/workshops/paper_143.pdf RDF - http://en.wikipedia.org/wiki/Resource_Description_Framework http://www2007.org/workshops/paper_143.pdf

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    14. 14 We discuss databases here as a whole (including the DB and frontend) Röhrender Hirsch auf einer Lichtung vor Fels Date1896AuthorMoritz Müller (1841–1899) http://commons.wikimedia.org/wiki/Image:Moritz_M%C3%BCller_-_R%C3%B6hrender_Hirsch.jpg http://commons.wikimedia.org/wiki/Image:Satan.jpgWe discuss databases here as a whole (including the DB and frontend) Röhrender Hirsch auf einer Lichtung vor Fels Date1896AuthorMoritz Müller (1841–1899) http://commons.wikimedia.org/wiki/Image:Moritz_M%C3%BCller_-_R%C3%B6hrender_Hirsch.jpg http://commons.wikimedia.org/wiki/Image:Satan.jpg

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    16. 16 CACTVS DB frontend is among the best CACTVS DB frontend is among the best

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    18. 18 Cytoscape http://cytoscape.org/screenshots/2_4_ss1.pngCytoscape http://cytoscape.org/screenshots/2_4_ss1.png

    19. 19 Helpful for getting overview with classificationsHelpful for getting overview with classifications

    20. 20 http://dx.doi.org/10.1186/1471-2105-7-176 Discuss Frameworks, Portals, Mashupshttp://dx.doi.org/10.1186/1471-2105-7-176 Discuss Frameworks, Portals, Mashups

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    22. 22 On Lipidmaps use the SDF file resource (unpack it from ZIP to SDF) (its free) On ChemAxon Instant JChem use the Download resource on the left (its free) On Biometa go to the download section and load the SDF (import as molecules) or import the flat txt as tables. Reaction data import is currently limited to the original chemistry reaction format (*.RDF)On Lipidmaps use the SDF file resource (unpack it from ZIP to SDF) (its free) On ChemAxon Instant JChem use the Download resource on the left (its free) On Biometa go to the download section and load the SDF (import as molecules) or import the flat txt as tables. Reaction data import is currently limited to the original chemistry reaction format (*.RDF)

    23. 23 Protein-Protein Interactions Metabolic Pathways Signaling Pathways Pathway Diagrams Transcription Factors / Gene Regulatory Networks Protein-Compound Interactions Genetic Interaction Networks Protein Sequence Focused Protein-Protein Interactions Metabolic Pathways Signaling Pathways Pathway Diagrams Transcription Factors / Gene Regulatory Networks Protein-Compound Interactions Genetic Interaction Networks Protein Sequence Focused

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    29. 29 CASH cow for non-profit American Chemical Society Advances in DB design in 70s/80s during time such databases were too large Subscription price annual between 80,000 Dollar (5 seats) and 200,000 Dollar (commercial) 250 million revenue (2006) Source:ChemspiderCASH cow for non-profit American Chemical Society Advances in DB design in 70s/80s during time such databases were too large Subscription price annual between 80,000 Dollar (5 seats) and 200,000 Dollar (commercial) 250 million revenue (2006) Source:Chemspider

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    36. 36 Hwk (*) LINGUISTIC RUIN? LOL! INSTANT MESSAGING AND TEEN LANGUAGE ; Tagliamonte and Denis; Amercian Speech; 83 (1): 3. (2008); DOI:10.1215/00031283-2008-001 Hwk (*) LINGUISTIC RUIN? LOL! INSTANT MESSAGING AND TEEN LANGUAGE ; Tagliamonte and Denis;Amercian Speech; 83 (1): 3. (2008); DOI:10.1215/00031283-2008-001

    37. 37 http://en.wikipedia.org/wiki/GNU_Free_Documentation_License http://en.wikipedia.org/wiki/GNU_Free_Documentation_License

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