Readings

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Contents

Formative Usability Test

  • balsamiq.com
  • usertesting.com
  • optimizely.com

Web Framework

http://hubzero.org/ HUBzero ® is a powerful, open source software platform for creating dynamic web sites that support scientific research and educational activities

Visualization

  • Joe Miller, acaciamulga.net (acaciamulga@gmail.com), taxonomy tree with characters. shows 10 characters along the species, aggregate character values at higher ranks, highlights variations of characters using vertical bars, link to distribution on a map. http://www.acaciamulga.net/#!phylojive-demo-trait-data/cwpe
  • Graph lib: Gephi https://gephi.org/ internally used GraphXML. Used by the Open Tree of Life. Load tens thousands of node efficient. Have different modules that emphasis differences or similarity.

Modeling

Glossaries and Ontologies

  • "TERMS FOR SURFACE VESTITURE AND RELIEF OF CUCURBITACEAE FRUITS"[1]
  • Ontology Modularization: Del Vescovo C, Gessler D, Klinov P, Parsia B, Sattler U, Schneider T, Winget A (2011). Decomposition and Modular Structure of BioPortal Ontologies. In Proceedings of the 10th International Semantic Web Conference ISWC 2011 (Part I) pp. 130-145 [2]
  • Gessler DDG, Joslyn C, Verspoor K. (2013) A Posteriori Ontology Engineering for Data-Driven Science. In Data Intensive Science, Eds. T. Critchlow, K. Kleese van Dam. CRC Press.
  • Phenotator: http://wwwdev.ebi.ac.uk/fgpt/phenotator/ (Use this tool to enter phenotypes descriptions and annotate these description with ontology terms using the entity/quality (EQ) pattern. An application ontology is generated automatically based on the annotations)

Parsing

  • Groza, Tudor, Jane Hunter, and Andreas Zankl. 2012. “Supervised Segmentation of Phenotype Descriptions for the Human Skeletal Phenome Using Hybrid Methods.” BMC Bioinformatics 13 (1) (October 15): 265.[3]

Pdf to Text

Semantic similarity/relatedness

Based on WordNet, provide path, depth, info content based measures, may include relatedness measures like lesk, vector, hso

WordNet::Similarity http://wn-similarity.sourcforge.net

NLTK http://nltk.org

ws4j https://code.google.com/p/ws4j/ [leaves large and leaves small has similarity of 100%, do not deal with antonyms]

Based on UMLS (Unified Medical Language System), provide path, depth, info content measures, includes relatedness measures lesk, vector

UMLS::Similarity http://umls-similarity.sourceforge.net

Based on (GO), provide path, depth, and info content measures

Proteinon http://lasige.di.fc.ul.pt/webtools/proteinon/

Semantic Assistants Wiki

Publication Venues

http://currents.plos.org/treeoflife/

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