Mercurial > repos > mikel-egana-aranguren > sadi_docker_workflow

comparison Galaxy-Workflow-SADI-Docker_use_case.ga @ 1:47db0b303a50 default tip

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Added annotations to workflow
author Mikel Egana <mikel.egana.aranguren@gmail.com>
date Mon, 07 Sep 2015 19:18:27 +0200
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0:22be3a551998 1:47db0b303a50
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "The workflow answers the following question: Given a set of UniProt proteins, which ones are related to PubMed abstracts containing the term ``brain'', and what are they KEGG entries? The workflow starts from a simple list of UniProt identifiers, and retrieves different datasets from a regular SADI service (to obtain KEGG entries) and a set of 3 OpenLifeData2SADI services (to obtain PubMed abstracts). The results are then merged and queried to obtain the KEGG entries of proteins that are related to PubMed abstracts that contain the term",
4 "format-version": "0.1",
5 "name": "SADI-Docker use case",
6 "steps": {
7 "0": {
8 "annotation": "Convert white spaces to tabs, so that Galaxy recognises the list of UniProt IDs as a column",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [],
12 "label": null,
13 "name": "Convert",
14 "outputs": [
15 {
16 "name": "out_file1",
17 "type": "tabular"
18 }
19 ],
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22 "top": 202.90626764297485
23 },
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26 "tool_id": "Convert characters1",
27 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"condense\": \"\\\"True\\\"\", \"strip\": \"\\\"True\\\"\", \"input\": \"null\", \"convert_from\": \"\\\"s\\\"\"}",
28 "tool_version": "1.0.0",
29 "type": "tool",
30 "user_outputs": [],
31 "uuid": "658762bb-9052-4dd2-bb6b-e77613a6dcfe"
32 },
33 "1": {
34 "annotation": "Convert UniProt identifiers to URIs: Add a column with the first part of the URI",
35 "id": 1,
36 "input_connections": {
37 "input": {
38 "id": 0,
39 "output_name": "out_file1"
40 }
41 },
42 "inputs": [],
43 "label": null,
44 "name": "Add column",
45 "outputs": [
46 {
47 "name": "out_file1",
48 "type": "input"
49 }
50 ],
51 "position": {
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57 "tool_id": "addValue",
58 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"http://openlifedata.org/uniprot:\\\"\", \"iterate\": \"\\\"no\\\"\"}",
59 "tool_version": "1.0.0",
60 "type": "tool",
61 "user_outputs": [],
62 "uuid": "c2421757-1d5d-435c-ac9e-fb036ccd4448"
63 },
64 "2": {
65 "annotation": "Convert UniProt identifiers to URIs",
66 "id": 2,
67 "input_connections": {
68 "input1": {
69 "id": 1,
70 "output_name": "out_file1"
71 }
72 },
73 "inputs": [],
74 "label": null,
75 "name": "Merge Columns",
76 "outputs": [
77 {
78 "name": "out_file1",
79 "type": "tabular"
80 }
81 ],
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90 "tool_version": "1.0.1",
91 "type": "tool",
92 "user_outputs": [],
93 "uuid": "63b4d2ff-0e1d-449d-aad5-a2ccd033d36a"
94 },
95 "3": {
96 "annotation": "Obtain the UniProt URIs",
97 "id": 3,
98 "input_connections": {
99 "input": {
100 "id": 2,
101 "output_name": "out_file1"
102 }
103 },
104 "inputs": [],
105 "label": null,
106 "name": "Cut",
107 "outputs": [
108 {
109 "name": "out_file1",
110 "type": "tabular"
111 }
112 ],
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116 },
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119 "tool_id": "Cut1",
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121 "tool_version": "1.0.2",
122 "type": "tool",
123 "user_outputs": [],
124 "uuid": "f3912f69-b561-4dd5-91f0-1e492e19bb9c"
125 },
126 "4": {
127 "annotation": "Add a column with the URI of the SADI service input OWL class",
128 "id": 4,
129 "input_connections": {
130 "input": {
131 "id": 3,
132 "output_name": "out_file1"
133 }
134 },
135 "inputs": [],
136 "label": null,
137 "name": "Add column",
138 "outputs": [
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140 "name": "out_file1",
141 "type": "input"
142 }
143 ],
144 "position": {
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152 "tool_version": "1.0.0",
153 "type": "tool",
154 "user_outputs": [],
155 "uuid": "c01e5509-2a60-4ad4-848c-b31f9ccfc841"
156 },
157 "5": {
158 "annotation": "Add a column with the URI of the SADI service input OWL class",
159 "id": 5,
160 "input_connections": {
161 "input": {
162 "id": 3,
163 "output_name": "out_file1"
164 }
165 },
166 "inputs": [],
167 "label": null,
168 "name": "Add column",
169 "outputs": [
170 {
171 "name": "out_file1",
172 "type": "input"
173 }
174 ],
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178 },
179 "post_job_actions": {},
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181 "tool_id": "addValue",
182 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"http://openlifedata.org/uniprot_vocabulary:Resource\\\"\", \"iterate\": \"\\\"no\\\"\"}",
183 "tool_version": "1.0.0",
184 "type": "tool",
185 "user_outputs": [],
186 "uuid": "98b1f088-3de5-4dbd-a655-63a630517e1a"
187 },
188 "6": {
189 "annotation": "Convert to RDF, adding the triple rdf:type input OWL class",
190 "id": 6,
191 "input_connections": {
192 "input_file": {
193 "id": 4,
194 "output_name": "out_file1"
195 }
196 },
197 "inputs": [],
198 "label": null,
199 "name": "SADI - Tab-to-RDF",
200 "outputs": [
201 {
202 "name": "output_file",
203 "type": "rdf"
204 }
205 ],
206 "position": {
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212 "tool_id": "SADI-Docker-tab2rdf",
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214 "tool_version": "0.1",
215 "type": "tool",
216 "user_outputs": [],
217 "uuid": "a05b8d4f-1b5f-4930-bd77-dfb5163b4556"
218 },
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220 "annotation": "Convert to RDF, adding the triple rdf:type input OWL class",
221 "id": 7,
222 "input_connections": {
223 "input_file": {
224 "id": 5,
225 "output_name": "out_file1"
226 }
227 },
228 "inputs": [],
229 "label": null,
230 "name": "SADI - Tab-to-RDF",
231 "outputs": [
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233 "name": "output_file",
234 "type": "rdf"
235 }
236 ],
237 "position": {
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243 "tool_id": "SADI-Docker-tab2rdf",
244 "tool_state": "{\"__page__\": 0, \"triples\": \"[{\\\"__index__\\\": 0, \\\"o_col\\\": \\\"\\\", \\\"o_type\\\": \\\"False\\\", \\\"s_col\\\": \\\"\\\", \\\"p_val\\\": \\\"http://www.w3.org/1999/02/22-rdf-syntax-ns#type\\\"}]\", \"input_file\": \"null\", \"output_format\": \"\\\"ntriples\\\"\", \"namespace\": \"{\\\"choose_namespace\\\": \\\"none\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null}",
245 "tool_version": "0.1",
246 "type": "tool",
247 "user_outputs": [],
248 "uuid": "217c654d-5353-4d93-a6de-c5c5bb205e64"
249 },
250 "8": {
251 "annotation": "Convert to RDF/XML syntax",
252 "id": 8,
253 "input_connections": {
254 "input_file": {
255 "id": 6,
256 "output_name": "output_file"
257 }
258 },
259 "inputs": [],
260 "label": null,
261 "name": "SADI - RDF Format (Rapper)",
262 "outputs": [
263 {
264 "name": "output_file",
265 "type": "rdf"
266 }
267 ],
268 "position": {
269 "left": 438.9826703071594,
270 "top": 200.90973138809204
271 },
272 "post_job_actions": {},
273 "tool_errors": null,
274 "tool_id": "SADI-Docker-rapper",
275 "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"rdfxml\\\"\", \"__rerun_remap_job_id__\": null, \"input_format\": \"\\\"ntriples\\\"\", \"input_file\": \"null\"}",
276 "tool_version": "0.1",
277 "type": "tool",
278 "user_outputs": [],
279 "uuid": "b5e1600e-a4ef-4ed6-a839-46bd1bcc59b3"
280 },
281 "9": {
282 "annotation": "Convert to RDF/XML syntax",
283 "id": 9,
284 "input_connections": {
285 "input_file": {
286 "id": 7,
287 "output_name": "output_file"
288 }
289 },
290 "inputs": [],
291 "label": null,
292 "name": "SADI - RDF Format (Rapper)",
293 "outputs": [
294 {
295 "name": "output_file",
296 "type": "rdf"
297 }
298 ],
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305 "tool_id": "SADI-Docker-rapper",
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307 "tool_version": "0.1",
308 "type": "tool",
309 "user_outputs": [],
310 "uuid": "995db5b3-4e12-48c8-bda0-f961861f008c"
311 },
312 "10": {
313 "annotation": "Execute SADI service to obtain KEGG entries",
314 "id": 10,
315 "input_connections": {
316 "input": {
317 "id": 8,
318 "output_name": "output_file"
319 }
320 },
321 "inputs": [],
322 "label": null,
323 "name": "SADI client",
324 "outputs": [
325 {
326 "name": "output",
327 "type": "rdf"
328 }
329 ],
330 "position": {
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333 },
334 "post_job_actions": {},
335 "tool_errors": null,
336 "tool_id": "SADI-Docker-sadi_client",
337 "tool_state": "{\"url\": \"\\\"http://sadiframework.org/services/getKEGGIDFromUniProt\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
338 "tool_version": "0.1",
339 "type": "tool",
340 "user_outputs": [],
341 "uuid": "01c2bbe7-a5e1-4bad-8c93-b01c6d0a5c8f"
342 },
343 "11": {
344 "annotation": "Execute SADI service to obtain HGNC entries",
345 "id": 11,
346 "input_connections": {
347 "input": {
348 "id": 9,
349 "output_name": "output_file"
350 }
351 },
352 "inputs": [],
353 "label": null,
354 "name": "SADI client",
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357 "name": "output",
358 "type": "rdf"
359 }
360 ],
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366 "tool_errors": null,
367 "tool_id": "SADI-Docker-sadi_client",
368 "tool_state": "{\"url\": \"\\\"http://biordf.org/cgi-bin/SADI/OpenLifeData2SADI/SADI/hgnc/uniprot_vocabulary_Resource_hgnc_vocabulary_x-uniprot-inverse_hgnc_vocabulary_Resource\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
369 "tool_version": "0.1",
370 "type": "tool",
371 "user_outputs": [],
372 "uuid": "ccdd413c-36be-48c3-96fc-4f233208a6b8"
373 },
374 "12": {
375 "annotation": "Execute SADI service to obtain OMIM entries",
376 "id": 12,
377 "input_connections": {
378 "input": {
379 "id": 11,
380 "output_name": "output"
381 }
382 },
383 "inputs": [],
384 "label": null,
385 "name": "SADI client",
386 "outputs": [
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388 "name": "output",
389 "type": "rdf"
390 }
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401 "type": "tool",
402 "user_outputs": [],
403 "uuid": "b7af50a8-a92a-44d9-bf1e-ca90cb69905d"
404 },
405 "13": {
406 "annotation": "Execute SADI service to obtain PubMed entries",
407 "id": 13,
408 "input_connections": {
409 "input": {
410 "id": 12,
411 "output_name": "output"
412 }
413 },
414 "inputs": [],
415 "label": null,
416 "name": "SADI client",
417 "outputs": [
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420 "type": "rdf"
421 }
422 ],
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429 "tool_id": "SADI-Docker-sadi_client",
430 "tool_state": "{\"url\": \"\\\"http://biordf.org/cgi-bin/SADI/OpenLifeData2SADI/SADI/omim/omim_vocabulary_Gene_omim_vocabulary_article_pubmed_vocabulary_PubMedRecord\\\"\", \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
431 "tool_version": "0.1",
432 "type": "tool",
433 "user_outputs": [],
434 "uuid": "3dcb6fc4-4021-4ea6-8e88-31c71d68699d"
435 },
436 "14": {
437 "annotation": "Merge all the inputs and outputs in single RDF graph: SADI only decorates inputs with new triples, so we can keep track of the whole process via URIs",
438 "id": 14,
439 "input_connections": {
440 "input_files_0|input_file": {
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442 "output_name": "output"
443 },
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448 "input_files_2|input_file": {
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460 "input_files_5|input_file": {
461 "id": 8,
462 "output_name": "output_file"
463 }
464 },
465 "inputs": [],
466 "label": null,
467 "name": "SADI - Merge RDF Graphs",
468 "outputs": [
469 {
470 "name": "output_file",
471 "type": "rdf"
472 }
473 ],
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485 "uuid": "7c24dd55-3032-4329-9fa3-734c963d8ed2"
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488 "annotation": "Query the merged RDF graph with the actual question",
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490 "input_connections": {
491 "ontology": {
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493 "output_name": "output_file"
494 }
495 },
496 "inputs": [],
497 "label": null,
498 "name": "SADI - Execute an SPARQL query against an RDF file",
499 "outputs": [
500 {
501 "name": "output",
502 "type": "html"
503 }
504 ],
505 "position": {
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507 "top": 461.92015266418457
508 },
509 "post_job_actions": {},
510 "tool_errors": null,
511 "tool_id": "SADI-Docker-SPARQLGalaxy",
512 "tool_state": "{\"out_format\": \"\\\"html\\\"\", \"__page__\": 0, \"pasted_query\": \"\\\"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \\\\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\\\\nPREFIX sadi: <http://sadiframework.org/ontologies/predicates.owl#>\\\\nPREFIX lsrn: <http://purl.oclc.org/SADI/LSRN/>\\\\n\\\\nSELECT ?protein ?label ?KEGG\\\\nWHERE { \\\\n?protein rdf:type lsrn:UniProt_Record . \\\\n?protein sadi:isEncodedBy ?KEGG . \\\\n?protein ?prot2hgnc ?hgnc . \\\\n?hgnc ?hgnc2omim ?omim . \\\\n?omim ?omim2pubmed ?pubmed . \\\\n?pubmed rdfs:label ?label . \\\\nFILTER (regex (?label, 'brain'))\\\\n}\\\"\", \"ontology\": \"null\", \"__rerun_remap_job_id__\": null}",
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519 "uuid": "8796e5be-1c91-4f91-9946-02a09a79401d"
520 }