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Items tagged with "xml" (20)

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Workflows (17)

Taverna 1 Original Uploader Andrea Wiggins	Data Set Metadata Generator (v1) Created: 19/08/08 @ 21:17:14 \| Last updated: 19/08/08 @ 21:25:53 Credits: Andrea Wiggins License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 144 times \| Downloaded: 57 times Tags (6): floss \| metadata \| open source software \| oss \| repository \| xml	View Download (v1)
Taverna 1 Original Uploader Bas Vroling	blastp using the MRS system (v1) Created: 28/11/08 @ 15:13:32 \| Last updated: 28/11/08 @ 15:34:19 Credits: Bas Vroling License: Creative Commons Attribution 3.0 Unported License This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database name. Valid database names that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb". Output is returned in XML. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 79 times \| Downloaded: 36 times Tags (4): BLAST \| protein \| similarity search \| xml	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	Search InChI in NCBI eSearch (pccompound) (v1) Created: 30/03/09 @ 09:26:25 \| Last updated: 30/03/09 @ 09:47:00 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 93 times \| Downloaded: 47 times Tags (12): bioinformatics \| compound \| compound info + image \| database \| image \| inchi \| information \| ncbi \| pccompound \| pubchem \| search \| xml	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	MassBank to KEGG (v1) Created: 30/03/09 @ 09:30:32 \| Last updated: 30/03/09 @ 09:49:13 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 198 times \| Downloaded: 0 times Tags (21): bget \| bioinformatics \| chemspider \| compound \| compound info + image \| database \| eutils \| image \| inchi \| information \| mass spectrometry \| massbank \| metabolomics \| ncbi \| pathway \| pccompound \| pubchem \| pug \| search \| summary \| xml	View
Taverna 1 Original Uploader Andrea Wiggins	DOI Record Generator (v1) Created: 29/04/09 @ 16:39:57 Credits: Andrea Wiggins Attributions: Data Set Metadata Generator License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow generates DOI record files for deposit, using data set metadata for the FLOSSmole project. It reads in an input file generated from a SQL query from an eprints database, and transforms the parts of the source file as necessary to create a comprehensive DOI deposit record. It also generates DOIs for the data sets. These metadata are inserted into an XML record template (based on the std-doi.xsd schema) and the individual resources are aggregated into a single file. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 107 times \| Downloaded: 32 times Tags (7): data management \| doi \| metadata \| repository \| sequence \| text \| xml	View Download (v1)
Taverna 1 Original Uploader Lebreton	retrieve protein sequence and do a BLAST and extract position from DDBJ Web services (v1) Created: 21/07/10 @ 13:10:40 \| Last updated: 21/07/10 @ 13:10:41 Credits: Lebreton Attributions: BLAST using DDBJ service License: Creative Commons Attribution-Share Alike 3.0 Unported License retrieve protein sequence and do a BLAST and extract position from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 10 times Tags (6): bioinformatics \| BLAST \| ddbj \| protein \| services \| xml	View Download (v1)
Taverna 2 Original Uploader Anja Le Blanc	Call VSO web service with HELIO input data (v1) Created: 04/08/10 @ 11:21:15 \| Last updated: 04/08/10 @ 11:22:26 Credits: Anja Le Blanc License: Creative Commons Attribution-Share Alike 3.0 Unported License date transformation from 2000-10-02T23:00:00 to 20001002230000 HELIO instrument names as in http://helio-dev.i4ds.ch/xsd/instruments.xsd spitt into source and instrument names; if these pair don't exist only first part (source) is tried. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 9 times Tags (4): astrophysics \| heliophysics \| solar \| xml	View Download (v1)
Taverna 2 Original Uploader Anja Le Blanc	instruments in sxr and euv spectrum (v1) Created: 20/08/10 @ 15:39:20 \| Last updated: 20/08/10 @ 15:39:22 Credits: Anja Le Blanc License: Creative Commons Attribution-No Derivative Works 3.0 Unported License ICS use case 5 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 13 times Tags (4): heliophysics \| solar \| votable \| xml	View Download (v1)
Taverna 2 Original Uploader Anja Le Blanc	retrive dpas data for all ics instruments for HEC event data (v1) Created: 14/09/10 @ 13:55:06 \| Last updated: 14/09/10 @ 13:59:12 Credits: Anja Le Blanc Attributions: Extracting data from VOTable format by using XPath query Retrieve all data for all instruments for a given periode of time License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow demonstrates the standard query there events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 11 times Tags (6): astrophysics \| heliophysics \| solar \| votable \| xml \| xpath	View Download (v1)
Taverna 2 Original Uploader Anja Le Blanc	retrive dpas data for all ics instruments for only a limited number (3 random) HEC event data (v1) Created: 14/09/10 @ 14:24:20 \| Last updated: 14/09/10 @ 14:24:24 Credits: Anja Le Blanc Attributions: retrive dpas data for all ics instruments for HEC event data License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow demonstrates the standard query where events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS. In this version data from only 3 random events (out of the HEC list) will be requested from the DPAS. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 12 times Tags (6): astrophysics \| heliophysics \| solar \| votable \| xml \| xpath	View Download (v1)
Taverna 1 Original Uploader trybik	Transform XML with parameters (v1) Created: 29/11/10 @ 11:45:52 \| Last updated: 29/11/10 @ 11:53:46 Credits: trybik License: Creative Commons Attribution-Share Alike 3.0 Unported License Similar to Transform_XML local widget but accepts transformation parameters and skips the part with writing to the output file. The essence, i.e. Transform_XML beanshell works with Strings representing file contents, not with file URLs. The XML transfomation parameters are given as a list of strings in the "param_name = param_value" format. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 18 times \| Downloaded: 16 times Tags (6): beanshell \| file \| transform \| xml \| xsl \| xslt	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	XPath Pubmed Ids (v2) Created: 23/03/11 @ 16:19:10 \| Last updated: 30/03/11 @ 09:28:13 Credits: Paul Fisher Attributions: XPath Pubmed Ids License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 25 times Tags (3): pubmed \| xml \| xpath	View Download (v2)
Taverna 2 Original Uploader Kalai	Download Structures from PubChem given chemical names (v1) Created: 24/05/11 @ 13:13:52 \| Last updated: 24/05/11 @ 14:19:24 Credits: Kalai Michael Gerlich Attributions: Download Entries from PubChem License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned. The pubchem compound_ID is then used to download structures from PubChem. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 19 times Tags (26): bioinformatics \| cheminformatics \| compound \| data \| download file \| esearch \| eutils \| file \| list \| ncbi \| open science \| open source \| pccompound \| split \| string \| structure \| structure retrieval \| synthetic \| taverna 2 \| taverna2 \| url2list \| workflow \| workflows \| wsdl \| xml \| xpath	View Download (v1)
Taverna 2 Original Uploader Chrisser	Latitude with beanshell (v1) Created: 06/10/11 @ 03:58:11 \| Last updated: 06/10/11 @ 04:32:39 Credits: Chrisser License: Creative Commons Attribution 3.0 Unported License This workflow takes in a string value or list of values and pulls out latitude coordinates formatted as ##-##(N or S) using the following regular expression: \d\d-\d\d(N\|S). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow contains primarily string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatting I requi... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 5 times Tags (10): input \| ist600 \| latitude \| netbeans \| regex \| string \| string_constant \| string_wrangling \| strings \| xml	View Download (v1)
Taverna 2 Original Uploader Chrisser	Longitude with beanshell (v1) Created: 06/10/11 @ 04:06:57 \| Last updated: 06/10/11 @ 04:29:35 Credits: Chrisser License: Creative Commons Attribution 3.0 Unported License This workflow takes in a string value or list of values and pulls out longitude coordinates formatted as ###-##(N or S) using the following regular expression: \d\d\d-\d\d(E\|W). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow primarily contains string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatti... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 5 times \| Downloaded: 4 times Tags (10): list \| longitude \| netbeans \| regex \| regular_expressions \| string \| string_constant \| string_wrangling \| strings \| xml	View Download (v1)
Taverna 2 Original Uploader Bharat Singh	EUADR Relationship Extraction Workflow (v1) Created: 27/07/11 @ 16:16:16 Credits: Bharat Singh License: Creative Commons Attribution-Share Alike 3.0 Unported License The workflow offers the ability to automatically determine if an ADR and a Drug are co-mentioned in any of the indexed resources. However the actual relationship between a Drug and an ADR can only be determined by referring to the actual resource The co-occurance relationship workflow seeks to automate the search for resources (publications, drug labels) related to ADRs corresponding to a given drug/ adverse event association. To enable this concept profiles for drugs and adverse effects wer... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 45 times \| Downloaded: 7 times Tags (22): adverse effects \| atc \| cui \| dailymed \| drug \| drug bank \| euadr \| html \| pubmed \| side effect \| xml	View Download (v1)
Taverna 2 Original Uploader Paul martin	Make XML Parameters (v1) Created: 08/02/12 @ 16:10:48 \| Last updated: 08/02/12 @ 16:12:39 Credits: Paul martin License: Creative Commons Attribution-Share Alike 3.0 Unported License Reformats a SNP list with optional p-value into the required XML input for the 'Define Associated Regions and Genes' workflow. Additional parameters can be supplied to add to the XML document. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 7 times \| Downloaded: 10 times Tags (2): define associated regions and genes \| xml	View Download (v1)