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688?size=60x60 Us M. Kirsh
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Blob Anthropology and Parallelism: The Individual as a Un...

Created: 2009-11-15 19:52:10

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

Abstract It is difficult to define perspective within sets that are self belonging. For example in the study of man­kind, anthropology, both men and their studies fall into the same category that contains the topic out­line. This situation entails a universal quality of uniqueness, an instance of it, to the topic of anthropo­logy that may be viewed in parallel with the topic of nature as the set of unique particulars. Yet one might assent to the notion in the inclusive study of m...

File type: Adobe PDF

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324?size=60x60 Gb George
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Blob Kegg Gene Identifiers

Created: 2009-11-14 16:29:01

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An example file of a list of Kegg gene identifiers used to test searching the Kegg database.

File type: Plain text

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324?size=60x60 Gb George
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Blob Pubmed Identifiers

Created: 2009-11-14 16:23:47

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A list of example pubmed identifers to use when testing abstract retrieval and text-mining workflows

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Avatar Gb Andrea
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Blob Very simple script to fix pathway commons biopax files

Created: 2009-11-04 11:05:46

Credits: User Andrea

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This very simple script (it only replace one type of ID!) will fix BioPAX files coming from PathwayCommons. In this files, rdf:ID is used instead of rdf:about, and since these files contains repetition, this results in an error in strict parsers. This error gets undetected in many system as they disable replicated ID checking for performance, but it's still a problem in some.

File type: application/x-perl

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4399?size=60x60 Gb Paul Fisher
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Blob KEGG Compounds to Inchi strings

Created: 2009-11-02 16:15:39 | Last updated: 2009-11-02 16:15:57

Credits: User Paul Fisher User Paul Dobson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of KEGG compounds which are reffered to by their Inchi strings.

File type: Chemistry Plan

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728?size=60x60 Nl Barend
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Blob The general plan and guidelines for BioAssist from O...

Created: 2009-10-26 10:15:03

Credits: User Barend

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document has been accepted at the NBIC management team meeting of 22 October 2009, and will serve as ageneral guideline to run the BioAssist program of NBIC. It might be a good idea to read the short document before you contact BioAssist for support in the scope of your 'code' or 'content' interests. Barend Mons

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728?size=60x60 Nl Barend
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Blob nano publication as a way to explain rich triples

Created: 2009-10-23 07:32:36 | Last updated: 2009-10-25 20:38:34

Credits: User Barend User Jan Velterop Network-member Concept Web Alliance (general)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This paper can be used to explain what triples in our context are meant to be and to serve I will present the paper on the semantic web conference workshop 26th of November

File type: application/x-download

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4399?size=60x60 Gb Paul Fisher
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Blob Ondex and Taverna Tutorial

Created: 2009-10-22 13:50:53 | Last updated: 2009-10-22 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

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688?size=60x60 Us M. Kirsh
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Blob Physical Contiguism

Created: 2009-10-18 05:28:32

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

The topic of physical contiguism is proposed in description to bridge paradoxes of mind and matter.  It seems that in efforts to bridge topics of science and consciousness focus has drifted towards a means to accommodate the mind in physical terms in order to draw correspondances with the more readily studied topic of matter. – i.e. as a topic in brain science. 

File type: Adobe PDF

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688?size=60x60 Us M. Kirsh
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Blob The Bend : A Speculation on History and Science

Created: 2009-09-20 04:08:33

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

The age of human civilization is given the name “the bend” based on a re-examination of the emergence of science, science theory content, and history.</font></font>  Civilization, existing over its course, in  darkness to the  nature of its partnership with the elements, oscillates in a romance that alternates between logical explanation, the rational, and illogical as they are  presented to him from the external. Its&rsquo...

File type: Adobe PDF

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469?size=60x60 Gb Paolo
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Blob GeoClouds workshop talk

Created: 2009-09-18 13:58:14

Credits: User Paolo User David De Roure User Carole Goble User David R Newman

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Indianapolis, IN, Sept 17, 2009 www.dataandsearch.org/dsi/events/geoclouds.html

File type: application/x-zip

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469?size=60x60 Gb Paolo
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Blob Provenance DB dump to be used as a reference

Created: 2009-09-10 14:18:23

Credits: User Paolo

License: Creative Commons Attribution-Share Alike 3.0 Unported License

this dump contains the provenance for 2 runs of this workflow: www.myexperiment.org/workflows/908

File type: Chemistry Plan

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688?size=60x60 Us M. Kirsh
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Blob Uniqueness , Self Belonging and Intercourse in Nature

Created: 2009-08-23 07:53:40 | Last updated: 2009-08-23 08:06:11

Credits: User M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

The world is discussed and framed so that it does not evolve divisions alike  the conceptual division  between Special and General Relativity in which emerged divides are   suggested to be parallel to and emerged from paradoxes of mind-matter, the self and nature.  Of all of the potential properties of the unique Universe, emergence, affinity, self avoidance , etc., self belonging is never a characteristic of unique and energy metabolizing spaces/entities.  ...

File type: Adobe PDF

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4399?size=60x60 Gb Paul Fisher
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Blob Pathway Term Enrichment Scores

Created: 2009-08-11 14:23:49

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of each pathway identified from day 7 post infection and linked to the Tir1 QTL. With each pathway is a list of terms that are common to both pathway and phenotype corpora. These terms were ranked accoring to their enrichement scores. The higher the score, the more significant the term is in relation to correlating the pathway with the African trypanosomiasis resistance phenotype.

File type: Plain text

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4399?size=60x60 Gb Paul Fisher
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Blob Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 14:15:58

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project. Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th...

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4399?size=60x60 Gb Paul Fisher
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Blob PubMed Term Counts

Created: 2009-08-11 13:59:35

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in MEDLINE the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.

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4399?size=60x60 Gb Paul Fisher
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Blob PubMed Abstract Number

Created: 2009-08-11 13:54:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the number of articles available in MEDLINE, through PubMed, at the time of performing these data analyses. The date of identifying these publications was 25/02/2009.

File type: Plain text

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Term Counts (in Phenotype Corpus)

Created: 2009-08-11 13:34:42 | Last updated: 2009-08-11 13:58:28

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in the phenotype corpus the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype.

File type: Plain text

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Concept Profile - Terms

Created: 2009-08-11 13:05:07 | Last updated: 2009-08-11 13:06:51

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model. These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl These terms represent the concept profile for the phenotype.

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4399?size=60x60 Gb Paul Fisher
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Blob Phenotype Abstracts for Trypanosomiasis Resistance

Created: 2009-08-11 12:45:24

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of published abstracts from MEDLINE, that are related to the African Trypanosomiasis resistance phentoype in the mouse. The term used in the PubMed search was: trypanosom* AND (tolerance OR resistance) . The workflow limited the date of the search using PubMed between 31/12/2005 to 01/01/2009, and was restricted to 500 abstracts.

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