Author_Publications_author_name00 Magnus Palmblad 2015-06-17 15:49:31.182 UTC The name of an author 2015-06-17 15:49:41.450 UTC chart0extract_id_for_cited_workxml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.5net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <responseWrapper><version>4.5.0.1</version><hitCount>62</hitCount><request><query>auth:"Magnus Palmblad" sort_date:y&amp;offSet=0</query><resultType>lite</resultType><synonym>false</synonym><page>1</page><pageSize>1000</pageSize></request><resultList><result><id>27086584</id><source>MED</source><pmid>27086584</pmid><title>Authentication of closely related fish and derived fish products using tandem mass spectrometry and spectral library matching.</title><authorString>Nessen MA, van der Zwaan DJ, Greevers S, Dalebout H, Staats M, Kok E, Palmblad M.</authorString><journalTitle>J Agric Food Chem</journalTitle><pubYear>2016</pubYear><journalIssn>0021-8561</journalIssn><pubType>journal 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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeoffSet_zerovalue00net.sf.taverna.t2.activitiesstringconstant-activity1.5net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedraw_chartcitations1publications1chart00 This Rshell takes as input (flattened) lists of years for the publications and citations of author_name and outputs two histograms, one for the publications and one for the citations, per year. 2015-09-14 16:28:34.699 UTC net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity publications 1 false citations 1 false chart 0 0 false localhost 6311 false false publications INTEGER_LIST citations INTEGER_LIST chart PNG_FILE 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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetCitationsid0pageSize0source0responseBody00net.sf.taverna.t2.activitiesrest-activity1.5net.sf.taverna.t2.activities.rest.RESTActivity GET http://www.ebi.ac.uk/europepmc/webservices/rest/{source}/{id}/citations/1/{pageSize} application/xml application/xml String false false false false true id java.lang.String source java.lang.String pageSize java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_id_for_cited_workxml_textsearchPublicationsresponseBodybuild_queryauthor_nameauthor_nameFlatten_Listinputlistextract_pubYear_for_citing_articlesnodelistextract_pubYear_for_citing_articlesxml_textgetCitationsresponseBodydraw_chartcitationsFlatten_Listoutputlistdraw_chartpublicationsextract_pubYear_for_all_worknodelistsearchPublicationsqueryStringbuild_queryqueryStringsearchPublicationsoffSetoffSet_zerovaluesearchPublicationspageSizearticles_to_retrievevaluesearchPublicationsresultTyperesultType_litevalueextract_pubYear_for_all_workxml_textsearchPublicationsresponseBodygetCitationsidextract_id_for_cited_worknodelistgetCitationspageSizeciting_articles_to_retrievevaluegetCitationssourcePubMed_and_MEDLINEvaluechartdraw_chartchart f3916175-2afa-4e94-9012-1087806d5d4f 2016-05-09 08:21:35.277 UTC 86de0556-3983-4da3-81c2-770d23ea8477 2015-09-14 14:23:12.911 UTC a20e45c0-4102-4a38-9d39-2b00c7c03c88 2015-09-14 14:44:58.15 UTC 70cf69c3-c2e2-4411-9a1f-20cad89c1aa0 2015-09-14 14:46:45.859 UTC 6e6fe540-3192-4221-a6d7-370911515b1d 2016-05-09 08:44:38.165 UTC d72d7b75-14e1-4aa5-a179-1b090ee2f22c 2015-06-17 14:47:41.206 UTC cf104017-de0c-4f35-bc7c-4ff5d2564841 2015-09-11 11:33:25.399 UTC bd67ef81-3d37-495e-afc0-72dce735dfa5 2015-09-11 11:35:22.345 UTC This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two REST calls are made. First, we "searchPublications" to retrieve the bibliographic records for all published work of a single author. Then, we "getCitations" to extract the year of all articles citing the work of this author. A conditional XPath is here used to only look up citing articles for cited work, i.e. records with result[citedByCount>0]. The pubYear fields is extracted from the raw Web Service results and fed to an Rshell that produces two histograms as output, one for publications and one for citations, very similar to the "Citation Report" in the Thomson Reuters Web of Science. This is a REST equivalent of the SOAP workflow www.myexperiment.org/workflows/4720.html. 2016-05-09 10:59:19.850 UTC 0ce3b0e2-ccda-4ac0-bf22-d1ed85cca271 2015-09-14 14:31:08.921 UTC bb984250-4ebb-4140-8dcf-a752557661a6 2015-09-14 16:28:34.813 UTC 7a553981-eae3-417b-9f3b-cb1873a431d7 2016-05-09 11:31:24.627 UTC 8c229ff8-0ea4-4589-a79a-d74ae268e461 2015-09-07 11:09:30.966 UTC 384475f1-0572-41ac-a485-a3eedb18463d 2015-06-17 15:49:48.583 UTC 0bd0ecdb-8459-40e7-94a8-4e5726183b8d 2015-09-14 13:52:48.711 UTC 33c81e10-61cd-42ac-8e83-058a935d1094 2015-06-17 15:17:42.126 UTC 72630699-e507-4a86-9dff-8199093ee0e6 2015-09-07 11:38:29.463 UTC 09e33109-9656-4d0f-a67c-0e1ef016c180 2015-09-14 16:31:06.363 UTC 5123be55-0e2e-46cd-a37e-3365ac2c7981 2015-09-14 13:35:53.911 UTC c43d4b2b-9219-49fa-b332-de2b3a34b545 2015-09-11 11:06:55.938 UTC 38d67a9b-0698-4db8-b1f7-6dc11a5d63fb 2015-09-07 11:22:10.705 UTC 9fe83e28-9efb-4595-abb9-6fefc544c916 2015-09-11 11:12:56.947 UTC 10d7966c-b99d-4c1e-a8a5-8ff138fa4471 2015-06-17 15:45:31.358 UTC 8852a376-0f8c-4e3d-88d4-8cf6d801cd22 2015-09-07 11:25:31.627 UTC Author Publications and Citations by Year with REST 2016-05-09 11:31:23.273 UTC de17cf39-56b7-4259-a564-e1dc6e7f8abb 2015-09-11 11:13:36.996 UTC 3236a7f2-7fd4-4f7d-9f14-902de831173b 2015-09-17 16:38:09.321 UTC 65ae77f0-5d4b-4147-a539-8489e03aea19 2015-06-17 14:33:05.146 UTC 9e6acb2a-c872-4de3-8ec1-44e6092051ad 2015-09-14 09:35:15.119 UTC 4ecd9bc6-77fc-4a09-8fbb-a8de52a73c1a 2015-09-11 11:23:32.9 UTC 9c9d05bd-5d98-4679-8f72-c0802cecab95 2015-09-14 09:45:04.643 UTC 7b2d8003-77ce-4f1d-8f31-aa5245c24550 2015-09-14 14:19:54.322 UTC 4729d116-3482-4ae9-9029-ba932485d36f 2015-06-17 15:48:39.671 UTC 7f16894d-8023-4c3e-9a0d-aaeae87b1b23 2016-05-09 11:27:44.115 UTC 767b33cf-2a10-4717-8bc0-80ef91da61bd 2015-06-17 14:45:24.545 UTC 64f9c2da-748b-4f5f-9deb-ff20b897653c 2015-09-14 13:41:30.407 UTC 49b50497-1aa9-45ae-b22c-914dc312f707 2015-06-17 15:05:10.52 UTC 0d039122-0f12-4c1e-aa6f-1b556fa907b5 2015-06-17 15:42:02.258 UTC 7b7abfe9-77a8-4131-b9ec-d5d9ed0ca3f8 2015-09-14 13:29:40.911 UTC 0cce7356-c5b8-489b-945a-cd795dd088d2 2015-09-11 11:16:05.338 UTC 3b11cf8a-57af-47b8-bf66-3abb9686f8a8 2015-09-14 13:34:12.577 UTC 9d7d9ee8-2230-4c1a-b023-f72228146ce7 2016-05-09 08:50:17.734 UTC 4539ac5a-3fe3-4088-86c7-e9f38eba4199 2016-05-09 08:35:05.146 UTC b75da20d-9e6c-475f-9e51-df8f16205fc8 2015-09-07 11:34:02.237 UTC 05835153-e64d-4157-ac2a-58a8ef5f82d7 2015-09-14 14:27:39.146 UTC 83920730-d196-4d35-a4f0-b498df439edf 2015-09-14 14:04:37.792 UTC 6bbd4637-7863-4d4e-8b25-011a42d911eb 2015-09-14 16:16:13.625 UTC 8627c922-ea66-45ae-8fbe-4a7b9614ead7 2015-09-14 16:23:47.475 UTC 5c2fe851-3ca8-41ac-b814-c28552a0a48c 2015-09-07 11:33:05.932 UTC 35f57c4d-991c-43aa-ab8e-9dd52f63f1d6 2015-09-14 13:55:09.597 UTC 26194012-eeea-4fab-9934-62d7a83199b0 2015-09-11 11:41:14.784 UTC 15b76c3e-980b-4498-bfad-4b563b0f9257 2015-06-17 15:06:27.191 UTC 2fa75b66-7aff-4719-afbe-0e171859b51e 2015-06-17 14:48:29.871 UTC c2727bb2-c0b2-40bb-81d6-7bc0bf56b498 2016-05-09 08:37:13.606 UTC ebb18c4a-c083-48f6-9f32-e880d6953ec1 2016-05-09 08:48:06.918 UTC d05e470c-ba0a-48a1-a2cf-b954f6ca5c43 2015-09-14 09:49:36.629 UTC f0d3e185-9f45-4a06-9eb5-00a648d2d7ff 2015-09-07 11:26:01.20 UTC Magnus Palmblad 2015-09-14 16:31:04.905 UTC e97b650a-3717-4a64-8b48-460f39d857f8 2015-09-14 14:45:50.962 UTC c5884e33-fb3b-41f1-89c4-d4aefd73bec1 2016-05-09 08:35:19.298 UTC 46f0cf5c-678c-4e05-8250-4e848a59b90b 2016-05-09 08:29:11.70 UTC c016aef9-1140-4565-be4c-26d6e6c51c63 2015-09-11 11:35:08.162 UTC d1d010ae-934f-4c85-a295-e98b6469ea68 2016-05-09 08:46:10.911 UTC 37c1d08e-22a8-438d-8c7b-a4a1a0a6e6d3 2015-06-17 15:30:33.882 UTC a90d411c-8da1-4469-b99e-7b28f8647851 2016-05-09 11:00:05.951 UTC cfb1581b-f62f-477a-8cf1-a61047bd0a62 2015-09-14 09:51:03.480 UTC cb1be238-dcf8-4043-a8a3-95383539eafc 2015-09-11 11:14:43.559 UTC 082dff52-a2b5-4f8f-b212-8807a903b4a8 2015-09-11 11:22:00.354 UTC db00d1bf-ba0d-4a56-9c66-18b2cb5e3005 2015-09-07 11:14:43.596 UTC eab96b96-0c4a-424e-8cc4-8ea8894519fe 2015-09-14 13:39:30.148 UTC 8748ac94-5f94-453d-9f66-48c611262d9a 2015-09-11 11:46:44.940 UTC 8c32cc05-cb12-4112-9992-e81bb4026d5a 2015-09-07 11:17:46.315 UTC 80b07576-4311-495d-9571-7de3dc6704c4 2015-09-11 11:49:06.680 UTC be914dc7-eed6-4f6a-b110-88703fc321db 2015-09-07 11:13:15.906 UTC 9fed8734-e020-46d0-910f-77bc118e326e 2016-05-09 08:51:13.1 UTC a3f7ec89-7485-42d2-a891-cd3842737cd3 2015-09-11 11:25:03.733 UTC 3795cff4-d941-4512-bd7c-ed495c315846 2015-09-11 11:20:58.988 UTC 131f876b-bedc-4846-8845-53eb62102ed1 2015-09-14 13:40:41.615 UTC fc3a1ad5-91c9-4e47-af12-0cd5823ba039 2015-09-11 11:11:40.593 UTC