Planet Bioclipse

my first #bioclipse plugin: A pubmed plugin

Anonymous, 15/05/2012 | Source: andrawaag's posterous

I haven't found an out of the box text-mining platform, where I push a button to launch the text mining resulting in a interesting set of "ore" or facts. It usually involves much preprocessing of text and efficient storage of intermediate results. @egonw recently introduced me to Bioclipse (http://bioclipse.net/). For what I have seen so far, Bioclipse looks like a promising platform to develop a "push-a-button" textmining. Whether this assumptions proofs to be true remains to be seen, but it is worth considering building a text mining platform for.

A a hello world exercise, I have started developing a pubmed plugin for Bioclipse. Pubmed remains a primary repository of biomedical scientific text, making it ideal starting point.

So far the following calls have been implemented.

findPubmedIdentifiers

This call takes a pubmed query (http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.How_do_I_search_PubM) and returns the resulting pubmed identifiers. By default the first 20 hits are returned. The maximum number of hits can be increased by giving the required number as a second parameter.

getFullTextLink

This call returns a URL pointing to a fulltext version of the given pubmed identifier

getPubMedAbstract

This call returns the abstract of a given pubmed identifier

getPubMedEntry

This call return the complete entry of a given pubmed identifier

loadPubMedEntryInBrowser

This call opens the pubmed entry of a given pubmed identifer in a webbrowser.

More function will follow soon.

The code is available: https://github.com/andrawaag/net.bioclipse.pubmed

Once installed the use of this plugin is strait forward.

Figure 1 shows a empty workbench in Bioclipse

When we type "pubmed." and subsequently type -->| (Tab). We get the available function calls.

We can now for example acquire the URL to the full text paper of any paper (e.g. on WikiPathways: 22096230)

and get:

More functions will follow.

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UML diagrams from the command line

, 28/04/2012 | Source: chem-bla-ics

I think I found a nice tool for my Groovy Cheminformatics book! And for Java documentation in general :) There are various tools to draw UML diagrams, such as umbrello, but the XMI format it uses is not easily edited from the command line, or included in books as source...

But I recently ran into UMLGraph on StackOverflow. I gave it a quick try but could not figure out how to get interfaces to show up. But Bob Cross pointed me to the right example:

#NBIC2012: Bioclipse-OpenTox

, 23/04/2012 | Source: chem-bla-ics

Tomorrow and Wednesday at the #NBIC2012 meeting (add your twitter account if your speaking or attending), I will demo Bioclipse-OpenTox during the Application Showcase sessions (all abstracts) (Tue: 10:00-11:15 and 14:50-15:50, Wed: 10:30-11:30 and 14:50-15:50). If you cannot attend (or just do not like Lunteren), watch these screencasts.

Abstract

Computational predictive toxicology draws knowledge from many independent sources, providing a rich support tool to assess a wide variety of toxicological properties. A key example would be for it to complement alternative testing methods. The integration of Bioclipse and OpenTox permits toxicity prediction based on the analysis of chemical structures, and visualization the substructure contributions to the toxicity prediction. This demo will focus on the application of Bioclipse in predictive toxicology, and show the interactive, visualization, and cloud computing features. There is an additional option for attendees to learn about how they can add their own predictive models.

Willighagen, E.L., Jeliazkova, N., Hardy, B., Grafström, R.C., Nov. 2011. Computational toxicology using the OpenTox application programming interface and bioclipse. BMC Research Notes 4 (487). http://www.biomedcentral.com/1756-0500/4/487

Chemical decision support with Chemspider and ChEMBL-RDF

Ola Spjuth, 19/04/2012 | Source: BioclipseBlog

Bioclipse Decision Support is a system where users can draw or import chemical structures, execute multiple predictions or database lookups, and visually interpret results. This was previously demonstrated for chemical liability assessment, and for running OpenTox predictions.

In the recent days I have implemented a module for adding a ChemSpider SimilaritySearch complemented by ChEMBL lookup via the ChEMBL-RDF data maintained by Egon Willighagen. In short this is how it operates:

Query ChemSpider using the SimilaritySearch via the Web API (SOAP).
For a maximum of 15 nearest neighbors in Chemspider, query ChEMBL-RDF for interactions, and present information about assays, targets, and interaction values.

Below you can find a screenshot of how it looks like in action. Now, the ChemSpider similarity search is rather slow (>30 s) but then again it takes a while to query 27 M chemical structures.

Note: This work was done against a development version of Chemspider Web API. You also need a security token in order to be able to query Chemspider; it's free and can be obtained here. When you have a security token, paste it into the Chemspider section of the Bioclipse preferences. The Chemspider + ChEMBL model for Bioclipse Decision Support will be part of the 2.6 release of Bioclipse, which we hope to have in place within a few weeks.

Thanks to Egon Willighagen (ChEMBL-RDF) and Valery Tkachenko (Chemspider) for aiding me in this work.

Postdoc position in predictive toxicology at Uppsala University

Ola Spjuth, 18/04/2012 | Source: BioclipseBlog

Postdoc position in cheminformatics, bioinformatics, or computer science - applications in predictive toxicology

We have an open postdoc position in the group of Pharmaceutical Bioinformatics at the Department of Pharmaceutical Biosciences, Uppsala University, Sweden.

The successful applicant will conduct research on data interoperability for predictive toxicology, and especially design and implement an infrastructure consisting of a database and user interfaces for data and predictive models in toxicology. Of particular interest will be to merge chemical and biological data within a semantic framework, and link toxicity data to genomics and metabolomics data (toxicogenomics) with a connection to the Bioclipse framework (www.bioclipse.net). PhD degree or equivalent scholarly competence in a relevant branch of chem/bioinformatics or computer science and a strong interest in informatics and data integration is required. Required competences include web programming, databases, and working knowledge in Java. Experience with linked data is desirable.

Deadline for application: May 9th , 2012.

Link to job ad and application form: http://www.uu.se/jobb/others/annonsvisning?tarContentId=186211&languageId=1

Lördags goodies #1: a Chemical Identifier Resolver plugin for Bioclipse

, 07/04/2012 | Source: chem-bla-ics

Saturdays is day where I am normally so tired, but my important inbox has gone down sufficiently, that I treated myself with some lördags goodies. So, I hacked up a Bioclipse plugin to interact with Markus Sitzmann's Chemical Identifier Resolver (here are his recent ACS slides). I'll post the code to my GitHub account shortly, and here's the obligatory screenshot:

The matching BSL script:

ui.open(cir.getByName("morphine"))

Also note the script log just above, where I searched for name. This returns multiple hits, but then I get a HTML page, making the command work. For now, I will inspect the content and check if it is HTML, other read it into a structure, and otherwise fail with a BioclipseException.

BiGCaT: Protein Structure

, 26/03/2012 | Source: chem-bla-ics

The last two weeks I have been busy with a course I gave last week (2x two hours lectures, 2x three hours practical) on Protein Structure. I had slides from last year at my disposal, but added some stuff, including a pointer to Google Play's page for the Jmol Android App (cool stuff!). The content involved the basic links between primary, secondary, tertiary, and quarternary structure.

At Maastricht University we use problem-based learning, and the topics for the students of this block (two bachelor studies) were aging and immunology. Interesting, because as a chemist I have limited background in these fields. Other content in this bioinformatics course done by our BiGCaT group involved SNPs, and I found a few interesting examples. As protein structure visualization tool, the course is using Yasara, a great tool, but next year I will prefer to use Bioclipse.

For the aging topic, I found a protein encoded by the WRN gene involved in Werner's Syndrome. I do not believe they found the actual cause of this disease yet, but that just makes it more interesting. The 3AAF structure in the PDB database (which, BTW, gets really slow when the USA wakes up), is associated with two SNPs:

So, it wasn't more than logical that I had the students visualize the residues and ask them to hypothesize which of the two was more likely to affect DNA binding:

Also very interesting to look at in this structure, is the π-π stacking by which this protein structure binds to the DNA:

OK, you really need to look at this yourself in 3D, but you see the Tyr and Phe binding to the DNA bases here :)

So, next year, one of these exercises will basically become a Bioclipse plugin with a nice cheat sheet. I also plan to finally write that plugin that educates people in the Jmol scripting language. Who wants to team up for that?

The other students got to look at the 3O4L structure (thanx to Patrick for the great topic!), which is a beautiful complex of protein structures from a normal cell (green and blue) and a T-cell (yellow and red):

In the middle is a small peptide (element colors), broken down by the normal cell from a Epstein-Barr virus. The membrane-bound protein parts are missing, but if you just imagine two huge cells on the left and right of this!

The red and yellow part are very similar structures, with a really nice S-S bond holding together the two subunits (all S-S bonds are depicted in magenta):

And this simple complex has many variants on the T-cell receptor side, allowing our human body to adapt to all sorts of viruses, etc. This is what life looks like! Isn't chemistry amazing!

Google Summer of Code 2012: CDK and Bioclipse project ideas

, 18/03/2012 | Source: chem-bla-ics

The NRNB +Google Summer of Code is primarily about +Cytoscape and Wikipathways / PathVisio (the latter two are co-developed in our BiGCaT group in Maastricht), but involves a few project ideas where the +Chemistry Development Kit and Bioclipse have an important role too:

IDEA 27: Extend PathVisio with a Plugin for Metabolomics-related Properties
IDEA 33: Substructure search and small molecule lookups within Cytoscape network

For Bioclipse, I wrote up these two project ideas:

IDEA 28: Integration of WikiPathways Visualization with PathVisio into Bioclipse
IDEA 29: Integration of Cytoscape into Bioclipse

I have been previously mentor, when Alexander worked on Strigi-Chemistry, desktop searching for chemistry, already 5 years ago!

Bioclipse and SADI

, 09/03/2012 | Source: chem-bla-ics

I do have to apologize to the Dumontier Lab... Michel visited us when I was still in Uppsala University (so, that's way too long ago), and we spoke about SADI, a really interesting framework for semantic computing. At thought that at the time, and I still do. But, I never got around to playing with it... but this week was so weird, I had to get my mind off... so, time for some random hacking...

Thus, a SADI manager (client) for Bioclipse. Why? Because I can. Two minutes to have the Bioclipse SDK set up a new plugin template, two hours to decide that one by one copying Maven dependencies is the worst waste of time ever, two minutes to figure out how git svn clone for just the last few Subversion commits works again, five minutes of cloning, two minutes of running mvn assembly:assembly, three minutes of figuring out what to add to the pom.xml again, one minute of running mvn assembly:single, and three minutes of waiting for the registry triples to be loaded after calling the Registry.getAllServices() method:

> sadi.listServices()
[http://sadiframework.org/examples/blast/Debaryomyces+hansenii, http://s5.semanticscience.org:8080/hbdc/hbdc, http://s7.semanticscience.org/~ben/cgi-bin/PlasmoDB/get_sequence_for_region, http://sadiframework.org/examples/blast/Nasonia+vitripennis, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsFinishingTimeInterval, http://unbsj.biordf.net/name-search-sadi/getSimilarICD9DiseaseNames, http://unbsj.biordf.net/ncbi-sadi/getSubclassesByNCBITaxonomyClassURI, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetPublicationRelatedGenes, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetStatus, http://sadiframework.org/examples/blast/Aedes+aegypti, http://unbsj.biordf.net/FISHTOX-SADIServices/RNA2DNAReverseTranscriber, http://sadiframework.org/examples/blast/Zea+mays, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NC2SequenceService, http://sadiframework.org/examples/blast/Chlamydomonas+reinhardtii, http://sadiframework.org/examples/blast/Encephalitozoon+cuniculi, http://sadiframework.org/examples/blast/Babesia+bovis, http://sadiframework.org/examples/blast/Eragrostis+tef, http://sadi-service.semanticscience.org/sadi-AptamerBase-REST-Wrapper/Aptamerbasegetaptamerwithsequencecollectionfromquery, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigenepublicationdate, http://sadiframework.org/examples/blast/Cryptosporidium+parvum, http://sadiframework.org/services/getPubMedReferencesForPDB, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getisoabbreviationfrompmid, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getdoifrompmid, http://unbsj.biordf.net/ncbi-sadi/getNCBITaxonomyIDByClassURI, http://s5.semanticscience.org:8080/computesas/mlogp, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXM2ZFIN, http://unbsj.biordf.net/mi-sadi/getMutationByWildtypeProtein, http://sadiframework.org/examples/ermineJgo, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantsymbol, http://unbsj.biordf.net/hmdb-sadi/getSMPDBIDByHMDBID, http://tomcat.dev.biordf.net/sadi-blast/snapdragon, http://dev.biordf.net/~kawas/cgi-bin/snp2gene, http://sadiframework.org/examples/blast/Allium+cepa, http://dev.biordf.net/~kawas/cgi-bin/getGOTermAssociationsPDB, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetDatabaseLinks, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXM2MGI, http://cbrass.biordf.net/hbac/hbac, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetPublicationRelatedPharmGKBEntities, http://sadiframework.org/examples/blast/Leishmania+braziliensis, http://sparql.tw.rpi.edu/services/datafaqs/faqt/void-triples, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-taxonomy/Taxid2scientificname, http://s5.semanticscience.org:8080/computesas/topsa, http://sadiframework.org/examples/blastUniprot, http://s7.semanticscience.org/~ben/cgi-bin/SGD/get_child_features, http://unbsj.biordf.net/name-search-sadi/getSimilarICD10ProcedureNames, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneVariantGeneSymbol, http://s5.semanticscience.org:8080/computesas/molfor, http://s5.semanticscience.org:8080/partialpolarsurfacearea/partialpolarsurfacearea, http://unbsj.biordf.net/FISHTOX-SADIServices/ZFIN2RefSeqProtein, http://s7.semanticscience.org/~ben/cgi-bin/CGD/get_features_overlapping_region, http://unbsj.biordf.net/hmdb-sadi/getHMDBIDByOMIMID, http://s7.semanticscience.org/~ben/cgi-bin/CryptoDB/get_child_features, http://unbsj.biordf.net/icd-sadi/getDiseaseClassByICD9ID, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantpostflanksequence, http://sadiframework.org/examples/entrezGene2Uniprot, http://sadiframework.org/examples/blast/Trichomonas+vaginalis, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_XP2RNAService, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDrugName, http://s5.semanticscience.org:8080/computesas/rncsa, http://unbsj.biordf.net/FISHTOX-SADIServices/AEExperiment2Platform, http://dev.biordf.net/~kawas/cgi-bin/entrezGene2pubmed, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetMass, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNP2UniProt, http://unbsj.biordf.net/FISHTOX-SADIServices/BLASTp2RefSeqProtein, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqAP2TAIR, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneRelatedPhenotypes, http://dev.biordf.net/~kawas/cgi-bin/getGOTermAssociationsENSEMBL, http://unbsj.biordf.net/ec-sadi/getEnzymeClassByECID, http://sadiframework.org/examples/blast/human, http://cbakerlab.unbsj.ca/lipids-sadi/getLMSDRecordBySMILES, http://sadiframework.org/examples/blast/Aspergillus+niger, http://sadiframework.org/examples/blast/Aspergillus+clavatus, http://sadiframework.org/examples/blast/Loxodonta+africana, http://sadiframework.org/examples/blast/Asparagus+officinalis, http://sadiframework.org/services/opencitations/getCitedArticles, http://unbsj.biordf.net/mi-sadi/getMIDBBioEntityByType, http://unbsj.biordf.net/mieo-sadi/getSingularAminoAcidChangeByHGVSDenotation, http://sadiframework.org/examples/blast/Solanum+tuberosum, http://sadiframework.org/examples/blast/Saccharomyces+cerevisiae, http://unbsj.biordf.net/mie-sadi/extractMutationInfoFromASCIIText, http://sadiframework.org/services/getGOTerm, http://unbsj.biordf.net/icd-sadi/getSubclassByICD9DiseaseClass, http://sadiframework.org/services/getKEGGGenesByPathway, http://unbsj.biordf.net/ncbi-sadi/getNCBITaxonomyClassByName, http://unbsj.biordf.net/name-search-sadi/getSimilarProteinNames, http://sadiframework.org/examples/linear, http://sadiframework.org/examples/blast/Paramecium+tetraurelia, http://s7.semanticscience.org/~ben/cgi-bin/SGD/get_feature_info, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqYP2ZFIN, http://s7.semanticscience.org/~ben/cgi-bin/CryptoDB/get_features_overlapping_region, http://sadiframework.org/examples/blast/Vigna+radiata, http://cbakerlab.unbsj.ca/lipids-sadi/getLMSDRecordByFormula, http://sadiframework.org/services/opencitations/getCitingArticles, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsAfterTimeInterval, http://unbsj.biordf.net/hmdb-sadi/getKEGGPATHWAYIDByHMDBID, http://s5.semanticscience.org:8080/computesas/wpsa3, http://unbsj.biordf.net/omim-sadi/getDiseaseNameByOMIMID, http://s5.semanticscience.org:8080/computesas/pisys, http://unbsj.biordf.net/lipid-class-sadi/classifyLipid, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetOntologyChildren, http://s6.semanticscience.org:8080/lac/lac, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDrugAttributes, http://sadiframework.org/services/getDrugBankByUniProt, http://sadiframework.org/examples/blast/Triticum+turgidum, http://unbsj.biordf.net/FISHTOX-SADIServices/AGILocusCodeRecord2GO, http://s6.semanticscience.org:8080/wiepan/wiepan, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getpublicationabstractfrompmid, http://unbsj.biordf.net/name-search-sadi/getSimilarDrugNames, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigeneorganismlineage, http://s5.semanticscience.org:8080/computesas/pnsa, http://dev.biordf.net/~kawas/cgi-bin/getKeggPathwaysByKeggDrug, http://s5.semanticscience.org:8080/computesas/ppsa2, http://cbakerlab.unbsj.ca/util-sadi-serv/pdf2ascii, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetStatus, http://s5.semanticscience.org:8080/wiepan/wiepan, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNP2TAIR, http://s7.semanticscience.org/~ben/cgi-bin/Gramene/get_parent_features, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/TestingVariants, http://unbsj.biordf.net/lipid-class-sadi/getLMLipidClassByLiProClass, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_YP2Record, http://unbsj.biordf.net/FISHTOX-SADIServices/IntActProtein2ProteinInteraction, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetPublicationRelatedDrugs, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetSecondaryId, http://unbsj.biordf.net/name-search-sadi/getSimilarDiseaseNames, http://sadiframework.org/examples/blast/Plasmodium+falciparum, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneRelatedDrugs, http://unbsj.biordf.net/icd-sadi/getICD9IDByDiseaseClassURI, http://sadiframework.org/examples/uniprot2omim, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNM2TAIR, http://sadiframework.org/examples/blast/Giardia+intestinalis, http://s5.semanticscience.org:8080/computesas/fpsa2, http://sadiframework.org/examples/blast/Plasmodium+chabaudi, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Gettitlefrompmid, http://unbsj.biordf.net/FISHTOX-SADIServices/CowEBIUniProtRecord2GO, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_YP2RNAService, http://s5.semanticscience.org:8080/computesas/rpc, http://s5.semanticscience.org:8080/molwt/molwt, http://sadiframework.org/examples/uniprotInfo, http://unbsj.biordf.net/FISHTOX-SADIServices/HumanEBIUniProtRecord2GO, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantfrequencies, http://s7.semanticscience.org/~ben/cgi-bin/CGD/get_child_features, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getcopyrightinformation, http://sadiframework.org/services/getDrugNames, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsOverlappingTimeInterval, http://sadiframework.org/services/opencitations/getCitingArticles, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneAlternateSymbols, http://sadiframework.org/examples/keggPathway2Compound, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiGetCitations, http://unbsj.biordf.net/mieo-sadi/getThreeLetterDenotationForSingularAminoAcidChange, http://s7.semanticscience.org/~ben/cgi-bin/ToxoDB/get_sequence_for_region, http://unbsj.biordf.net/omim-sadi/getOMIMIDByName, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getlanguagefrompmid, http://s7.semanticscience.org/~ben/cgi-bin/ToxoDB/get_parent_features, http://sparql.tw.rpi.edu/services/datafaqs/faqt/internet-domain, http://unbsj.biordf.net/din-sadi/getDINByATCDrugClass, http://s5.semanticscience.org:8080/computesas/fpsa1, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigeneinfo, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetOntologyChildren, http://sadiframework.org/examples/blast/Ovis+aries, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneRelatedPathways, http://sadiframework.org/services/getKEGGOrthologsByGene, http://unbsj.biordf.net/util-sadi-serv/getKeggPathwayByName, http://sadiframework.org/examples/blast/Equus+caballus, http://s5.semanticscience.org:8080/computesas/pnsa2, http://sadiframework.org/examples/blast/Triticum+aestivum, http://s7.semanticscience.org/~ben/cgi-bin/AmoebaDB/get_parent_features, http://unbsj.biordf.net/lipids-sadi/getLMLipidCategoryByLMLipidClass, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigeneencodingproteindescription, http://unbsj.biordf.net/FISHTOX-SADIServices/BLASTx2RefSeqProtein, http://s5.semanticscience.org:8080/xlogp/xlogp, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NM2ProteinService, http://unbsj.biordf.net/icd-sadi/getDiseaseClassByICD10CAID, http://sadiframework.org/services/getGeneByAllele.pl, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsBeforeTimeInterval, http://s7.semanticscience.org/~ben/cgi-bin/CryptoDB/get_sequence_for_region, http://sadiframework.org/examples/blast/Caenorhabditis+briggsae, http://unbsj.biordf.net/FISHTOX-SADIServices/BLASTn2RefSeqRNA, http://dev.biordf.net/~kawas/cgi-bin/getDragonAlleleDescription, http://s5.semanticscience.org:8080/computesas/rnc, http://s5.semanticscience.org:8080/computesas/wpsa2, http://cbrass.biordf.net/sadi-examples/PressureInmmHg, http://dev.biordf.net/~kawas/cgi-bin/getPubmedIDsByKeggPathway, http://unbsj.biordf.net/util-sadi-serv/getPMIDByKeyPhrase, http://sadiframework.org/services/getCanadianSpeciesObservationsFromTaxonID, http://unbsj.biordf.net/lipids-sadi/getHMDBIDByLMID, http://dev.biordf.net/~kawas/cgi-bin/getCHEBIEntryFromKEGGCompound, http://s5.semanticscience.org:8080/computesas/lobmax, http://sadiframework.org/examples/blast/Drosophila+pseudoobscura, http://s6.semanticscience.org:8080/bondcount/bondcount, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetInchi, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXR2MGI, http://s5.semanticscience.org:8080/computesas/fcomp, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetFormulae, http://sadiframework.org/services/getRefSeqEntriesByKEGG, http://sadiframework.org/examples/blast/Brassica+napus, http://unbsj.biordf.net/FISHTOX-SADIServices/SGDRecord2GO, http://s5.semanticscience.org:8080/computesas/dpsa3, http://sparql.tw.rpi.edu/services/datafaqs/core/select-faqts/via-sparql-query, http://unbsj.biordf.net/ncbi-sadi/getNCBITaxonomyClassByID, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevarianttype, http://unbsj.biordf.net/mi-sadi/getProteinPropertyByType, http://unbsj.biordf.net/lipids-sadi/getLMSDRecordByCommonName, http://sadiframework.org/examples/blast/rat, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NM2Record, http://unbsj.biordf.net/pacs-sadi/getImageByPersonName, http://sadiframework.org/examples/blast/Leishmania+major, http://sadiframework.org/examples/blast/Caenorhabditis+elegans, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NS2SequenceService, http://s5.semanticscience.org:8080/computesas/cwppsa, http://sadiframework.org/examples/blast/Schizosaccharomyces+pombe, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetCitations, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NW2SequenceService, http://sadiframework.org/services/opencitations/getAbstract, http://unbsj.biordf.net/lipids-sadi/getLMIDByPubChemSubstanceID, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetEntityStar, http://sadiframework.org/examples/blast/Saccoglossus+kowalevskii, http://s5.semanticscience.org:8080/computesas/wnsa3, http://sparql.tw.rpi.edu/services/datafaqs/faqt/redirect-loop, http://sadiframework.org/examples/blast/Manihot+esculenta, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsStartedByTimeInterval, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetChemicalStructures, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NP2Record, http://sadiframework.org/examples/blast/Oryza+sativa, http://s6.semanticscience.org:8080/aromaticatomcount/aromaticatomcount, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetDatabaseLinks, http://dev.biordf.net/~kawas/cgi-bin/getEnzymeGeneComponentParts, http://s6.semanticscience.org:8080/tpsa/tpsa, http://sadiframework.org/examples/blast/Ciona+intestinalis, http://s7.semanticscience.org/~ben/cgi-bin/TriTrypDB/get_child_features, http://sadiframework.org/examples/blast/Beta+vulgaris, http://s6.semanticscience.org:8080/sadi-soap-vrnafold-distance/Vrnafolddistancecalculator, http://dev.biordf.net/~kawas/cgi-bin/kegg2prosite, http://unbsj.biordf.net/din-sadi/getDrugProductNameByDINDrugProduct, http://cbakerlab.unbsj.ca/util-sadi-serv/getHTMLByPMCID, http://unbsj.biordf.net/mieo-sadi/getSingularAminoAcidChangeByOneLetterDenotation, http://unbsj.biordf.net/mi-sadi/visualiseMutationSeries, http://sadiframework.org/examples/blast/Sorghum+bicolor, http://sadiframework.org/services/getAllelesByGene.pl, http://unbsj.biordf.net/FISHTOX-SADIServices/SpeciesName2AEExperimentalRecord, http://sadiframework.org/examples/keggGene2GeneXrefs, http://sadiframework.org/examples/uniprot2prosite, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXP2ZFIN, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NP2SequenceService, http://unbsj.biordf.net/lipids-sadi/getLMSDRecordByLMLipidClass, http://unbsj.biordf.net/uniprot-sadi/getUniProtIDByRefSeqNPAccession, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXP2TAIR, http://unbsj.biordf.net/din-sadi/getDrugProductByDIN, http://unbsj.biordf.net/FISHTOX-SADIServices/ZFIN2RefSeqRNA, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-taxonomy/Taxid2genbankcommonname, http://unbsj.biordf.net/util-sadi-serv/getPDFByPMID, http://dev.biordf.net/~kawas/cgi-bin/getEcGeneComponentPartsHuman, http://unbsj.biordf.net/temporal-reasoning-sadi/getDurationOfTimeInterval, http://unbsj.biordf.net/din-sadi/getMonographByDINDrugProduct, http://dev.biordf.net/~kawas/cgi-bin/getUniprotByKeggGene, http://unbsj.biordf.net/util-sadi-serv/getUniProtIdByProteinName, http://s7.semanticscience.org/~ben/cgi-bin/CGD/get_sequence_for_region, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDrugVaClassification, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsFinishedByTimeInterval, http://unbsj.biordf.net/lipids-sadi/getLMIDByKEGGCompoundID, http://cbakerlab.unbsj.ca/util-sadi-serv/getPMCIDByPMID, http://s7.semanticscience.org/~ben/cgi-bin/PlasmoDB/get_features_overlapping_region, http://sadiframework.org/services/opencitations/getAbstract, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetEntityStar, http://sparql.tw.rpi.edu/services/datafaqs/faqt/predicate-counter, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantpharmgkbid, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetInchi, http://sadiframework.org/examples/hello-param, http://unbsj.biordf.net/FISHTOX-SADIServices/HMMR3PFamA, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNG2MGI, http://sadiframework.org/examples/blast/Eimeria+maxima, http://s7.semanticscience.org/~ben/cgi-bin/TriTrypDB/get_features_overlapping_region, http://s7.semanticscience.org/~ben/cgi-bin/VectorBase/get_sequence_for_region, http://s5.semanticscience.org:8080/alogp/alogp, http://unbsj.biordf.net/util-sadi-serv/getPMIDByPMCID, http://unbsj.biordf.net/FISHTOX-SADIServices/ZFIN2RefSeqDNA, http://sadiframework.org/examples/keggGene2Pathway, http://sadiframework.org/services/getMolecularInteractions, http://unbsj.biordf.net/lipids-sadi/getProteinRelatedToLMLipidCategory, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetMass, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NG2SequenceService, http://sadiframework.org/examples/blast/Theobroma+cacao, http://sadiframework.org/examples/blast/Medicago+sativa, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getauthorsfrompmid, http://sadiframework.org/examples/blast/Felis+catus, http://unbsj.biordf.net/ec-sadi/getEnzymeClassByName, http://cbakerlab.unbsj.ca/util-sadi-serv/getPDFByPMCID, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantpreflanksequence, http://unbsj.biordf.net/uniprot-sadi/getUniProtIDByEC, http://sadiframework.org/services/opencitations/getDocumentInfo, http://unbsj.biordf.net/mieo-sadi/getSingularAminoAcidChangeByThreeLetterDenotation, http://unbsj.biordf.net/pdb-sadi/blastPDB, http://sadiframework.org/examples/blast/Pan+troglodytes, http://unbsj.biordf.net/FISHTOX-SADIServices/UniProtRecord2IntAct, http://sadiframework.org/examples/blast/Brassica+juncea, http://sadiframework.org/examples/blast/Tribolium+castaneum, http://unbsj.biordf.net/FISHTOX-SADIServices/Feature2Sequence, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetCitations, http://s7.semanticscience.org/~ben/cgi-bin/SGD/get_features_overlapping_region, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NR2SequenceService, http://s5.semanticscience.org:8080/computesas/pjn, http://unbsj.biordf.net/lipids-sadi/getLMSDRecordByLipidMass, http://sadiframework.org/examples/linear-async, http://s7.semanticscience.org/~ben/cgi-bin/TriTrypDB/get_feature_info, http://s6.semanticscience.org:8080/sadi-soap-vrnafold/ViennaRNAFold, http://sadiframework.org/services/opencitations/getCitedArticles, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNM2ZFIN, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqZP2ZFIN, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NP2RNAService, http://unbsj.biordf.net/util-sadi-serv/pdf2ascii, http://unbsj.biordf.net/FISHTOX-SADIServices/DNA2RNATranscriber, http://unbsj.biordf.net/hmdb-sadi/getOMIMIDByHMDBID, http://sadiframework.org/examples/blast/Hordeum+bulbosum, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalBetween, http://unbsj.biordf.net/atc-sadi/getSubclassByATCDrugClass, http://sadiframework.org/examples/blast/Eremothecium+gossypii, http://sadiframework.org/examples/blast/Hordeum+vulgare, http://sadiframework.org/examples/uniprot2pubmed, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetSecondaryId, http://unbsj.biordf.net/ec-sadi/getECIDByEnzymeClassURI, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetIupacName, http://sadiframework.org/examples/pubmed2uniprot, http://unbsj.biordf.net/uniprot-sadi/getUniProtIDByProteinName, http://unbsj.biordf.net/hmdb-sadi/getHMDBIDBySMPDBID, http://sadiframework.org/examples/uniprot2EntrezGene, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNR2ZFIN, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigeneorganismcommonname, http://s5.semanticscience.org:8080/inchi2smiles/inchi2smiles, http://sadiframework.org/examples/blast/Canis+lupus+familiaris, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_AC2SequenceService, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNM2MGI, http://unbsj.biordf.net/util-sadi-serv/getGOTermByName, http://s5.semanticscience.org:8080/computesas/fpsa3, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigenelocation2, http://sadiframework.org/services/getKEGGPathwayDiagram, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneRelatedEntities, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsOverlappedByTimeInterval, http://unbsj.biordf.net/uniprot-sadi/getPMIDByUniProtID, http://unbsj.biordf.net/util-sadi-serv/getHTMLByPMCID, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NM2SequenceService, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetComments, http://unbsj.biordf.net/din-sadi/getAHFSDrugClassByDINDrugProduct, http://s7.semanticscience.org/~ben/cgi-bin/FlyBase/get_sequence_for_region, http://unbsj.biordf.net/icd-sadi/getICD9DiseaseClassByName, http://s5.semanticscience.org:8080/computesas/cwpnsa, http://unbsj.biordf.net/units-sadi/convertToKilograms, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_XP2Record, http://s7.semanticscience.org/~ben/cgi-bin/ToxoDB/get_child_features, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetDefinition, http://s7.semanticscience.org/~ben/cgi-bin/CGD/get_parent_features, http://sadiframework.org/examples/blast/Trypanosoma+brucei, http://unbsj.biordf.net/kegg-sadi/getATCClassByKEGGDRUGID, http://unbsj.biordf.net/hmdb-sadi/getHMDBIDByKEGGPATHWAYID, http://s7.semanticscience.org/~ben/cgi-bin/FlyBase/get_features_overlapping_region, http://sadiframework.org/examples/blast/Glycine+max, http://sadiframework.org/examples/blast/Tetrahymena+thermophila, http://sadiframework.org/examples/uniprot2go, http://unbsj.biordf.net/icd-sadi/getICD10CAIDByDiseaseClassURI, http://sadiframework.org/examples/blast/Arabidopsis+thaliana, http://sadiframework.org/examples/blast/Meleagris+gallopavo, http://sadiframework.org/examples/blast/Oreochromis+niloticus, http://unbsj.biordf.net/lipids-sadi/getLMSDRecordBySystematicName, http://sadiframework.org/examples/blast/Kluyveromyces+lactis, http://s5.semanticscience.org:8080/computesas/rpcsa, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsDuringTimeInterval, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantgenotypingexperiment, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneAlternateNames, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetPublicationRelatedDiseases, http://unbsj.biordf.net/util-sadi-serv/getGIByUniProtID, http://sadiframework.org/examples/blast/mouse, http://unbsj.biordf.net/FISHTOX-SADIServices/ORFPredictor, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneVariantsBySymbol, http://dev.biordf.net/~kawas/cgi-bin/getEnzymeGeneComponentPartsHuman, http://unbsj.biordf.net/hmdb-sadi/getPMIDByHMDBID, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqZP2TAIR, http://unbsj.biordf.net/FISHTOX-SADIServices/ZFINRecord2GO, http://unbsj.biordf.net/uniprot-sadi/getRefSeqNPAccessionByUniProtID, http://s7.semanticscience.org/~ben/cgi-bin/AmoebaDB/get_sequence_for_region, http://s6.semanticscience.org:8080/sadi-owlimqueryer/Owlimqueryer, http://dev.biordf.net/~kawas/cgi-bin/getEnzymeGeneComponentPartsMouse, http://s5.semanticscience.org:8080/computesas/vamd, http://sadi-service.semanticscience.org/sadi-AptamerBase-REST-Wrapper/Aptamerbasegetaptamerwithsequencefromid, http://sadiframework.org/examples/blast/Ustilago+maydis, http://s7.semanticscience.org/~ben/cgi-bin/ToxoDB/get_features_overlapping_region, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetRegistryNumbers, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_AP2SequenceService, http://sadiframework.org/examples/blastUniprotById, http://unbsj.biordf.net/lipid-class-sadi/mineTextForLipidInfo, http://sparql.tw.rpi.edu/services/datafaqs/core/select-faqts/identity, http://unbsj.biordf.net/units-sadi/convertToGrams, http://sadiframework.org/examples/blast/Physcomitrella+patens, http://sadiframework.org/examples/calculateBMI, http://unbsj.biordf.net/FISHTOX-SADIServices/UniProtRecord2GO, http://sadiframework.org/examples/blast/Scheffersomyces+stipitis, http://sadiframework.org/examples/entrezGene2Kegg, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetChebiAsciiName, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-taxonomy/Gettaxidrank, http://s5.semanticscience.org:8080/computesas/eccen, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-taxonomy/Taxid2commonname, http://sadiframework.org/examples/blast/Brassica+rapa, http://sadiframework.org/examples/blast/Plasmodium+berghei, http://sadiframework.org/examples/blast/Bos+taurus, http://dev.biordf.net/~kawas/cgi-bin/getKeggPathwaysByEnzyme, http://sparql.tw.rpi.edu/services/datafaqs/faqt/void-properties, http://s5.semanticscience.org:8080/computesas/fnsa1, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-taxonomy/Ncbieutilstaxonomy, http://sadiframework.org/examples/pubmed2uniprot, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigenealternatesymbols, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_XP2SequenceService, http://unbsj.biordf.net/FISHTOX-SADIServices/AGILocusCodeRecord2Sequence, http://sadiframework.org/services/getAlleleDescription.pl, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseAttributes, http://s7.semanticscience.org/~ben/cgi-bin/CGD/get_feature_info, http://sadiframework.org/examples/blast/Setaria+italica, http://s7.semanticscience.org/~ben/cgi-bin/Gramene/get_feature_info, http://sadiframework.org/examples/blast/Arabidopsis+lyrata, http://dev.biordf.net/~kawas/cgi-bin/getEnzymesEncodedByKeggGenes, http://sadiframework.org/examples/blast/Gibberella+zeae, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetSmiles, http://unbsj.biordf.net/lipids-sadi/getKEGGCompoundIDByLMID, http://sadi-service.semanticscience.org/sadi-AptamerBase-REST-Wrapper/Aptamerbasegetaptamerwithsequence, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXM2UniProt, http://s7.semanticscience.org/~ben/cgi-bin/AmoebaDB/get_feature_info, http://sadiframework.org/examples/blast/Lotus+japonicus, http://sadiframework.org/examples/uniprot2pdb, http://sadiframework.org/examples/blast/Sus+scrofa, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigeneencodingproteinname, http://unbsj.biordf.net/lipid-ref-sadi/getPublicationByLiProClass, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseName, http://unbsj.biordf.net/kegg-sadi/getKEGGDRUGIDByATCClass, http://cbakerlab.unbsj.ca/lipids-sadi/getLMSDRecordByLMID, http://sadiframework.org/examples/blast/Amphimedon+queenslandica, http://sadiframework.org/examples/blast/Dictyostelium+discoideum, http://unbsj.biordf.net/lipids-sadi/getLMSDRecordByFormula, http://s7.semanticscience.org/~ben/cgi-bin/PlasmoDB/get_feature_info, http://sparql.tw.rpi.edu/services/datafaqs/core/select-datasets/by-ckan-group, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_XM2Record, http://unbsj.biordf.net/ec-sadi/getSubclassByEnzymeClass, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_XM2SequenceService, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantsnptype, http://sadiframework.org/examples/blast/Solanum+lycopersicoides, http://unbsj.biordf.net/mi-sadi/getMutationByMutantProtein, http://s5.semanticscience.org:8080/computesas/fnsa2, http://s7.semanticscience.org/~ben/cgi-bin/FlyBase/get_child_features, http://s5.semanticscience.org:8080/computesas/dpsa1, http://sadiframework.org/examples/blast/Cryptosporidium+hominis, http://unbsj.biordf.net/FISHTOX-SADIServices/EnrichmentService, http://s7.semanticscience.org/~ben/cgi-bin/CryptoDB/get_parent_features, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_XM2ProteinService, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsStartingTimeInterval, http://cbrass.biordf.net/sadi-examples/calcBMIX, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqAP2ZFIN, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseGenericNames, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigenexrefs, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneSymbol, http://unbsj.biordf.net/icd-sadi/getSubclassByICD10CADiseaseClass, http://sadiframework.org/services/getKEGGCompoundsByPathway, http://sadiframework.org/examples/blast/Solanum+melongena, http://dev.biordf.net/~kawas/cgi-bin/getGOTermByGeneID, http://dev.biordf.net/~kawas/cgi-bin/getdbSNPRecordByUniprotID, http://sadiframework.org/examples/blast/Populus+trichocarpa, http://sadiframework.org/services/DragonServices/getDragonSimpleAnnotatedImages, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXM2TAIR, http://sadiframework.org/services/opencitations/getDocumentInfo, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_XR2SequenceService, http://unbsj.biordf.net/name-search-sadi/getSimilarATCDrugClassNames, http://sadiframework.org/examples/blast/Lolium+perenne, http://sadiframework.org/examples/blast/Medicago+truncatula, http://sadiframework.org/examples/blast/Brassica+nigra, http://sadiframework.org/examples/hello, http://s6.semanticscience.org:8080/wiponu/wiponu, http://unbsj.biordf.net/din-sadi/getATCDrugClassByDINDrugProduct, http://s5.semanticscience.org:8080/computesas/fnsa3, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXP2UniProt, http://sadiframework.org/examples/blast/Cryptococcus+neoformans, http://sadiframework.org/examples/blast/Ornithorhynchus+anatinus, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigenename, http://sadiframework.org/examples/blast/Vitis+vinifera, http://sadiframework.org/examples/blast/Aegilops+tauschii, http://unbsj.biordf.net/lipids-sadi/getPubChemSubstanceIDByLMID, http://sadiframework.org/services/renderProteinStructure, http://s7.semanticscience.org/~ben/cgi-bin/Gramene/get_child_features, http://sadiframework.org/examples/blast/Theileria+parva, http://dev.biordf.net/~kawas/cgi-bin/getEcGeneComponentPartsRat, http://s5.semanticscience.org:8080/zindex/zindex, http://sadiframework.org/examples/blast/Monodelphis+domestica, http://unbsj.biordf.net/uniprot-sadi/getUniProtIDByPMID, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetRegistryNumbers, http://sadiframework.org/examples/uniprot2kegg, http://sadiframework.org/examples/blast/Neurospora+crassa, http://sadiframework.org/examples/blast/Hydra+magnipapillata, http://s5.semanticscience.org:8080/computesas/pjtsis, http://unbsj.biordf.net/units-sadi/convertToMeters, http://cbrass.biordf.net/sadi-examples-cardio/patientrecord, http://sadiframework.org/examples/blast/Acyrthosiphon+pisum, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigeneorganismtaxname, http://sadiframework.org/examples/blast/Taeniopygia+guttata, http://s5.semanticscience.org:8080/computesas/wpsa1, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneRelatedDiseases, http://sadiframework.org/examples/blast/Strongylocentrotus+purpuratus, http://unbsj.biordf.net/FISHTOX-SADIServices/LocusHistoryService, http://dev.biordf.net/~kawas/cgi-bin/getDragonAlleleLocus, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqXR2ZFIN, http://sadiframework.org/examples/blast/Brassica+oleracea, http://unbsj.biordf.net/util-sadi-serv/getWikipediaPageByTopic, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetMolecularEntityWithIdentifier, http://sadiframework.org/examples/blast/Ailuropoda+melanoleuca, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetInchiKey, http://s7.semanticscience.org/~ben/cgi-bin/FlyBase/get_parent_features, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDrugGenericNames, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNR2MGI, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigenesymbol, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneName, http://unbsj.biordf.net/lipids-sadi/getLMIDByCHEBIID, http://s5.semanticscience.org:8080/computesas/thsa, http://unbsj.biordf.net/name-search-sadi/getSimilarOrganismNames, http://sadiframework.org/examples/blast/Guillardia+theta, http://sadiframework.org/examples/blast/Plasmodium+yoelii, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getstatusfrompmid, http://s5.semanticscience.org:8080/computesas/ip, http://unbsj.biordf.net/mi-sadi/getMutationByImpact, http://sparql.tw.rpi.edu/services/datafaqs/faqt/access/in-sparql-endpoint, http://sadiframework.org/services/getDragonSequenceLocus.pl, http://unbsj.biordf.net/atc-sadi/getDrugClassByATCID, http://dev.biordf.net/~markw/cgi-bin/services/DragonDB_Blast.pl, http://unbsj.biordf.net/uniprot-sadi/getProteinNameByUniProtID, http://sadiframework.org/examples/blast/Nomascus+leucogenys, http://sadiframework.org/examples/blast/Anolis+carolinensis, http://dev.biordf.net/~kawas/cgi-bin/getEcEncodedByKeggGenes, http://sadiframework.org/examples/blast/Xenopus+(Silurana)+tropicalis, http://s6.semanticscience.org:8080/sadi-rest-ncbi-eutils-gene/Getncbigenepublications, http://sadiframework.org/examples/blast/Aegilops+umbellulata, http://unbsj.biordf.net/lipids-sadi/getLMLipidClassById, http://unbsj.biordf.net/util-sadi-serv/getPMCIDByPMID, http://dev.biordf.net/~kawas/cgi-bin/getDragonLocusAlleles, http://unbsj.biordf.net/atc-sadi/getATCDrugClassByName, http://unbsj.biordf.net/mieo-sadi/getOneLetterDenotationForSingularAminoAcidChange, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-taxonomy/Taxid2synonym, http://unbsj.biordf.net/mi-sadi/visualiseMutationSeriesWithHomologyModeling, http://s7.semanticscience.org/~ben/cgi-bin/AmoebaDB/get_features_overlapping_region, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_ZP2Record, http://s7.semanticscience.org/~ben/cgi-bin/TriTrypDB/get_sequence_for_region, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNC2MGI, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getmedlinejournalcitationfrompmid, http://sparql.tw.rpi.edu/services/datafaqs/core/augment-datasets/with-preferred-uri-and-ckan-meta-void, http://dev.biordf.net/~kawas/cgi-bin/getEcGeneComponentPartsMouse, http://cbakerlab.unbsj.ca/lipids-sadi/getLMSDRecordBySystematicName, http://s5.semanticscience.org:8080/computesas/wnsa2, http://s7.semanticscience.org/~ben/cgi-bin/PlasmoDB/get_child_features, http://sadiframework.org/examples/y4x, http://unbsj.biordf.net/FISHTOX-SADIServices/AEExperiment2Info, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetSmiles, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getdatecreatedfrompmid, http://sadiframework.org/services/soroush/PressureConvertor, http://s5.semanticscience.org:8080/computesas/rhsa, http://s7.semanticscience.org/~ben/cgi-bin/SGD/get_parent_features, http://s7.semanticscience.org/~ben/cgi-bin/Gramene/get_sequence_for_region, http://s7.semanticscience.org/~ben/cgi-bin/FlyBase/get_feature_info, http://dev.biordf.net/~kawas/cgi-bin/getEnzymeGeneComponentPartsRat, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_YP2SequenceService, http://sadiframework.org/examples/blast/Avena+sativa, http://sadiframework.org/examples/blast/Phaseolus+vulgaris, http://sparql.tw.rpi.edu/services/datafaqs/faqt/discuss/contributor-email, http://s7.semanticscience.org/~ben/cgi-bin/AmoebaDB/get_child_features, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNM2UniProt, http://unbsj.biordf.net/mieo-sadi/getHGVSDenotationForSingularAminoAcidChange, http://unbsj.biordf.net/hmdb-sadi/getHMDBIDByPMID, http://sadiframework.org/examples/blast/Cricetulus+griseus, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseRelatedPhenotypes, http://unbsj.biordf.net/lipids-sadi/getCHEBIIDByLMID, http://unbsj.biordf.net/mi-sadi/getMutationImpactByProteinProperty, http://sadiframework.org/examples/blast/Danio+rerio, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetInchiKey, http://unbsj.biordf.net/mi-sadi/getMutationSubseries, http://sparql.tw.rpi.edu/services/datafaqs/faqt/sparql-service-description/named-graphs, http://sadiframework.org/examples/blast/Bombus+terrestris, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDrugStructure, http://sadiframework.org/examples/blast/Solanum+peruvianum, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseRelatedGenes, http://sadiframework.org/services/getKEGGParalogsByGene, http://sadiframework.org/services/getKEGGIDFromUniProt, http://sadiframework.org/services/HelloWorld, http://unbsj.biordf.net/FISHTOX-SADIServices/AERecord2Microarray, http://training.biordf.net/luke-sadi-services/Calculate+BMI, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getarticleissnfrompmid, http://dev.biordf.net/~kawas/cgi-bin/getGOTermDefinitions, http://cbakerlab.unbsj.ca/lipids-sadi/getLMSDRecordByLipidMass, http://sadiframework.org/examples/pdb2uniprot, http://sadiframework.org/examples/blast/Hemiselmis+andersenii, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetGeneAttributes, http://dev.biordf.net/~kawas/cgi-bin/kegg2pfam, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqNP2ZFIN, http://s5.semanticscience.org:8080/computesas/lobmin, http://sadiframework.org/examples/blast/Anopheles+gambiae, http://s7.semanticscience.org/~ben/cgi-bin/ToxoDB/get_feature_info, http://dev.biordf.net/~kawas/cgi-bin/getKeggPathwaysByEC, http://sadiframework.org/examples/blast/Capsicum+annuum, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqZP2UniProt, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-taxonomy/Getparenttaxidfromtaxid, http://s7.semanticscience.org/~ben/cgi-bin/PlasmoDB/get_parent_features, http://s6.semanticscience.org:8080/sadi-soap-vrnafold-heat/Vrnaheatcalculator, http://sadiframework.org/examples/blast/Magnaporthe+oryzae, http://sparql.tw.rpi.edu/services/datafaqs/faqt/lodcloud/max-1-topic-tag, http://unbsj.biordf.net/util-sadi-serv/getKeggDrugByName, http://unbsj.biordf.net/lipids-sadi/getLMIDByHMDBID, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseRelatedEntities, http://unbsj.biordf.net/FISHTOX-SADIServices/MGIRecord2GO, http://sadiframework.org/examples/blast/Pongo+abelii, http://sadiframework.org/examples/blast/Apis+mellifera, http://sadiframework.org/examples/blast/Leishmania+infantum, http://unbsj.biordf.net/atc-sadi/getATCIDByDrugClassURI, http://sadiframework.org/examples/blast/Candida+glabrata, http://sadiframework.org/examples/keggPathway2Gene, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseAlternateNames, http://s7.semanticscience.org/~ben/cgi-bin/Gramene/get_features_overlapping_region, http://sadiframework.org/examples/blast/Macaca+mulatta, http://sadi-service.semanticscience.org/sadi-AptamerBase-REST-Wrapper/Aptamerbasegetaptamerwithsequencefromname, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_ZP2RNAService, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NZ2SequenceService, http://sadiframework.org/services/getEntrezGeneIDsFromRefSeqTranscripts, http://sadiframework.org/examples/blast/Callithrix+jacchus, http://s5.semanticscience.org:8080/computesas/dpsa2, http://s7.semanticscience.org/~ben/cgi-bin/SGD/get_sequence_for_region, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsMeetingTimeInterval, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_ZP2SequenceService, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/Getgenevariantstrandsense, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetFormulae, http://unbsj.biordf.net/util-sadi-serv/getDOIDTermByName, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetSynonym, http://dev.biordf.net/~kawas/cgi-bin/getGeneInformation, http://sadiframework.org/examples/blast/Cavia+porcellus, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetOntologyParents, http://s5.semanticscience.org:8080/computesas/wnsa1, http://sadiframework.org/examples/blast/Eimeria+tenella, http://unbsj.biordf.net/icd-sadi/getICD10CADiseaseClassByName, http://unbsj.biordf.net/FISHTOX-SADIServices/InterProScan2GO, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsMetByTimeInterval, http://unbsj.biordf.net/uniprot-sadi/getECByUniProtID, http://s5.semanticscience.org:8080/apol/apol, http://s6.semanticscience.org:8080/sadi-ChEBI-soap-wrapper/ChebiSoapGetDefinition, http://unbsj.biordf.net/din-sadi/getDINDrugProductByDrugProductName, http://s7.semanticscience.org/~ben/cgi-bin/TriTrypDB/get_parent_features, http://unbsj.biordf.net/FISHTOX-SADIServices/WBRecord2GO, http://unbsj.biordf.net/FISHTOX-SADIServices/NCBI_NT2SequenceService, http://sadiframework.org/examples/blast/Solanum+lycopersicum, http://unbsj.biordf.net/temporal-reasoning-sadi/getTimeIntervalsContainingTimeInterval, http://s5.semanticscience.org:8080/computesas/pjgsis, http://dev.biordf.net/~kawas/cgi-bin/getGOTermAssociations, http://sadiframework.org/examples/blast/Gallus+gallus, http://unbsj.biordf.net/name-search-sadi/getSimilarKeggPathwayNames, http://sadiframework.org/examples/blast/Prunus+dulcis, http://sadiframework.org/examples/keggCompound2PubChem, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetOntologyParents, http://unbsj.biordf.net/FISHTOX-SADIServices/RefSeqAP2UniProt, http://unbsj.biordf.net/mi-sadi/mineTextForMutationImpacts, http://sadiframework.org/examples/blast/Oryctolagus+cuniculus, http://sadiframework.org/services/getTaxIDFromUniProt, http://unbsj.biordf.net/util-sadi-serv/getPDFByPMCID, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetChemicalStructures, http://unbsj.biordf.net/lipids-sadi/getLMLipidCategoryRelatedToProtein, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDiseaseRelatedPathways, http://sadi-service.semanticscience.org/PharmGKB-SADI-Wrapper/GetDrugTradeNames, http://sadiframework.org/examples/blast/Quercus+robur, http://s7.semanticscience.org/~ben/cgi-bin/CryptoDB/get_feature_info, http://s5.semanticscience.org:8080/moref/moref, http://sadiframework.org/examples/blast/Secale+cereale, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getaffiliationfrompmid, http://sadiframework.org/examples/blast/Bubalus+bubalis, http://dev.biordf.net/~kawas/cgi-bin/getEcGeneComponentParts, http://sadiframework.org/examples/blast/Yarrowia+lipolytica, http://unbsj.biordf.net/lipids-sadi/getLMSDRecordBySMILES, http://cbakerlab.unbsj.ca/util-sadi-serv/getPMIDByPMCID, http://sadi-service.semanticscience.org/sadi-rest-ncbi-eutils-pubmed/Getpaginationfrompmid, http://sadiframework.org/examples/blast/Aspergillus+fumigatus, http://unbsj.biordf.net/name-search-sadi/getSimilarLipidNames, http://sadiframework.org/examples/blast/Drosophila+melanogaster, http://unbsj.biordf.net/lipids-sadi/getLMSDRecordByLMID, http://sadi-service.semanticscience.org/sadi-ChEBI-soap-wrapper/ChebiSoapGetChebiAsciiName, http://unbsj.biordf.net/lipids-sadi/getLMLipidClassByName]

The code is available from the bioclipse.rdf repository.

Visualization of Life Science data with Java (Apache 2.0)

, 06/03/2012 | Source: chem-bla-ics

Daniel Swan pointed me to this blog post with a rather interesting title: Exploring multiple cancer genomics alterations with Gitools. The Gitools is more than a library, but just the visualization seems interesting already.

(The image comes from their website, and is licensed CC-BY.)

Gitools itself is licensed Apache 2.0 and I am wondering if we can reuse this in other projects, e.g. Bioclipse.