A Kalderimis - InterMine: Embeddable datamining components
0 likes519 views
InterMine is an integrated data warehouse with an optimizing query engine. It provides web services and embeddable widgets to make powerful data querying accessible to non-technical users. InterMine runs databases for various model organisms and is working to make machine-readable APIs and data displays universally accessible.
![from intermine.webservice import Service
s = Service(‘www.flymine.org/query’)
q = s.model.Gene.select(‘*’, ‘proteins.proteinDomains.*’)
.where(‘pathways’, ‘LOOKUP’, ‘pentose*’)
for row in q.rows():
print row[‘name’], row[‘proteins.proteinDomains.name’]
Saturday, 14 July 2012](https://image.slidesharecdn.com/intermine-embedding-bosc-2012-120714181613-phpapp02/85/A-Kalderimis-InterMine-Embeddable-datamining-components-9-320.jpg)
![Now it’s your turn!
<div id=”the-table-goes-here”></div>
<script>
(function($, im) {
var s, q, v;
s = new im.Service({ root: ‘www.flymine.org/query’, token: ‘MYTOKEN’ });
var q = {
from: ‘Gene’,
select: [‘symbol’, ‘proteins.proteinDomains.*’],
where: [{pathways: {LOOKUP: ‘pentose*’}]
};
var v = new im.query.results.CompactView(s, q);
v.$el.appendTo(‘#the-table-goes-here’);
v.render();
})(jQuery, intermine);
</script>
Saturday, 14 July 2012](https://image.slidesharecdn.com/intermine-embedding-bosc-2012-120714181613-phpapp02/85/A-Kalderimis-InterMine-Embeddable-datamining-components-16-320.jpg)
A Kalderimis - InterMine: Embeddable datamining components
- 1. InterMine Embeddable Data-Mining Widgets Saturday, 14 July 2012
- 2. InterMine is: • An integrated data-warehouse • An optimising and caching query engine • A set of web services • A suite of embeddable widgets Saturday, 14 July 2012
- 3. You are here User Scripts and Programs List Widgets Tables Ruby Web- Java Perl Python JS Application Web-Services Internal API Object Store Saturday, 14 July 2012
- 4. Who runs InterMine? InterMOD • FlyMine (D. melanogaster) • YeastMine (S. cerevisiae) • modMine • RatMine (R. norvegicus) • metabolicMine • ZfinMine (D. rerio) • TargetMine • Wormbase (C. elegans) • mitoMine • MGI (M. musculus) Also: S. pombe, FlyBase,TAIR Saturday, 14 July 2012
- 5. Prime strengths • Flexibility • Performance Saturday, 14 July 2012
- 6. Making it accessible • Make running a large data-warehouse accessible to groups with limited resources • Make powerful querying accessible to non-technical users • Make a machine readable API accessible to anyone • Make the display of data accessible through any site Saturday, 14 July 2012
- 7. Step 1 • Build web services platform and library support Saturday, 14 July 2012
- 8. from intermine.webservice import Service s = Service(‘www.flymine.org/query’) q = s.model.Gene.select(‘*’, ‘proteins.proteinDomains.*’) .where(‘pathways’, ‘LOOKUP’, ‘pentose*’) for gene in q: print gene.symbol for protein in gene.proteins: for domain in protein.proteinDomains: print domain.name Saturday, 14 July 2012
- 9. from intermine.webservice import Service s = Service(‘www.flymine.org/query’) q = s.model.Gene.select(‘*’, ‘proteins.proteinDomains.*’) .where(‘pathways’, ‘LOOKUP’, ‘pentose*’) for row in q.rows(): print row[‘name’], row[‘proteins.proteinDomains.name’] Saturday, 14 July 2012
- 10. Step 2 • Build Tools on this Platform Saturday, 14 July 2012
- 11. Table Widgets Saturday, 14 July 2012
- 12. Analysis Widgets Saturday, 14 July 2012
- 13. Step 3 • Eat own dog-food Saturday, 14 July 2012
- 14. Saturday, 14 July 2012
- 15. Danger, Danger! • live demo here... Saturday, 14 July 2012
- 16. Now it’s your turn! <div id=”the-table-goes-here”></div> <script> (function($, im) { var s, q, v; s = new im.Service({ root: ‘www.flymine.org/query’, token: ‘MYTOKEN’ }); var q = { from: ‘Gene’, select: [‘symbol’, ‘proteins.proteinDomains.*’], where: [{pathways: {LOOKUP: ‘pentose*’}] }; var v = new im.query.results.CompactView(s, q); v.$el.appendTo(‘#the-table-goes-here’); v.render(); })(jQuery, intermine); </script> Saturday, 14 July 2012
- 17. Toolkit Bootstrap Saturday, 14 July 2012
- 18. One stop shop: • All files served from cdn.intermine.org ➡Dependencies (jquery, backbone, bootstrap) ➡im.js ➡im-tables.js ➡widgets.js Saturday, 14 July 2012
- 19. Alex Kalderimis, Daniela Butano, Adrian intermine.org Carr , Sergio Contrino, Hu Fengyuan, Systems Biology Centre, University of Cambridge, Mike Lyne, Rachel Lyne, Julie Sullivan, Tennis Court Road, Cambridge CB2 1QR, UK Radek !t"pán, Gos Micklem +44 1223 760262 dev@intermine.org Saturday, 14 July 2012