PLOS Visualization Project
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The document describes a visualization of PLoS data created by mapping PLoS thesaurus terms to an existing map of all science created from Scopus data. It discusses mapping terms directly and indirectly, analyzing coverage by journal and year, and using the maps and underlying data to answer questions posed by PLoS about trends, relationships between fields, and how PLoS coverage compares to other databases. Visualizations are created in software like Pajek and Gephi and are meant to facilitate communication around science structure and metrics.
PLOS Visualization Project
- 1. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents Visualizing PLoS Data DHUG 2014 February 11, 2014 Kevin Boyack, Bob Kasenchak, Margie Hlava
- 2. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 2 AGENDA Background Data Science mapping Mapping thesaurus directly Mapping thesaurus indirectly » SciTech S&T map » Thesaurus map Overlays
- 3. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 3 BACKGROUND To answer questions posed by PLoS using PLoS index (thesaurus) terms, a map of the thesaurus space is desirable » Where is the coverage thin, where is it dense? » What areas are core and which are emerging trends? Which fields are growing quickly? » Which fields are interrelated? » Which fields have low activity but are related to very active fields? Some questions require more than PLoS data » How does the coverage in PLoS journals relate to coverage in other databases? A map of the thesaurus space can function as a template upon which various distributions can be overlaid Some questions are more amenable to tables than maps
- 4. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 4 DATA Thesaurus » 10,551 unique terms in 15,164 locations » 11 top level terms » 296 second level terms in 305 locations PLoS article data parsed / indexed by Access Innovations » Article level data through mid-2013; 84,989 records » 72,796 records with index (thesaurus) terms; 171,181 terms Scopus data » SciTech Strategies licenses use of Scopus data from Elsevier » 1996-2011; 25M records
- 5. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 5 THESAURUS STRUCTURE Biology CS Earth Env Eng Medicine People Physical Methods SS
- 6. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 6 SCIENCE MAPPING A map is a visual representation of the relationships within a » Classification system (e.g., journal categories, taxonomy) » Document corpus Science maps can/have been created using » Documents, Journals, Authors, Terms, Taxonomies 30-40 year tradition of science mapping » Well-established methodologies » Current computing power and data availability enable large scale mapping and analysis Maps used for communication, strategy, planning, evaluation … » Understanding of structure, relative location » Basis for metrics
- 7. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 7 GENERAL PROCESS Select data source and objects (e.g., docs) of interest Scopus / WoS PubMed Patents Your own data Calculate similarity between objects (doc-doc) Citations (links) Words (title/abstr) Create a visual layout (map) of the objects / clusters Pajek / Gephi
- 8. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 8 MAPPING PLOS TERMS DIRECTLY Mapped second level terms » All terms rolled up to the second level term at the top of the branch Cosine similarity between terms based on co-occurrence in articles Map created using Fruchterman-Reingold mapping routine in Pajek » Based on only the top 3 links per term – strongest linkages Each node (term) colored using top level terms » Biology and life sciences (light green) » Medicine and health sciences (salmon) » Physical sciences (purple) » Research and analysis methods (yellow) » Social sciences (light orange) » …
- 9. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 9 MAPPING PLOS TERMS
- 10. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 10 MAPPING PLOS TERMS DIRECTLY Resulting map is difficult to use » Using second level terms leaves out needed detail » Term counts span several orders of magnitude – hard to map well » Terms within the same branch of the thesaurus don’t cluster well Resulting map doesn’t account well for context (areas where PLoS has low coverage) Need a map that does a better job of providing context, and that better matches our current picture of science So … we decided to index Scopus data using the PLoS rule-base and map based on that more inclusive context
- 11. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 11 MAPPING PLOS TERMS INDIRECTLY Use existing map of all of science Triangulate term positions
- 12. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 12 SCITECH S&T MAP 20 million articles (1996-2011) 3 million patents (1996-2011) 220,000 document clusters Cluster contents using citation Cluster positions using text The visual is the final step (last 10%); the full process is needed for robust analysis Template on which other info can be overlaid; documents (and related info) tied to map positions We are the only ones in the world who do contextual analysis at this scale
- 13. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 13 TRIANGULATION Use full S&T map as basis Based on Scopus 2007-2011 Locate each thesaurus term as the average position of its documents The resulting map contains 11,934 terms; full coverage; interpretable Terms with multiple colors appear multiple times The term map becomes the basemap
- 14. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 14 THESAURUS BASEMAP The term map becomes the basemap Circle size - # documents Circle color – top level term Many small circles – detailed thesaurus and rule base that differentiates Few large circles – broad terms and rule base that doesn’t differentiate Location/size of terms facilitates questions - Is term well located in the thesaurus? - Is the rule base acting as desired? - Should term be broken up?
- 15. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 15 NOT JUST PRETTY PICTURES All visualizations are based on tabular data Pictures help form hypotheses Detailed analysis provides answers
- 16. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 16 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places Social sciences Science policy Circuit models Chromatin immunoprecipitation Evolutionary modeling Electron transport chain Intelligence Language Cognition Decision making
- 17. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 17 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places Social sciences Science policy
- 18. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 18 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places Social sciences Science policy
- 19. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 19 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places Social sciences Science policy
- 20. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 20 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places Social sciences Science policy
- 21. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 21 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places Social sciences Science policy
- 22. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 22 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places Social sciences Science policy
- 23. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 23 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences People and places Social sciences Science policy
- 24. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 24 ANALYSES Biology and life sciences Computer and information sciences Earth sciences Ecology and environmental sciences Engineering and technology Medical and health sciences Physical sciences Research and analysis methods People and places
- 25. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 25 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 26. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 26 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 27. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 27 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 28. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 28 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 29. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 29 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 30. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 30 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 31. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 31 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 32. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 32 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 33. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 33 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 34. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 34 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 35. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 35 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 36. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 36 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 37. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 37 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 38. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 38 ANALYSES PLoS – All journals and years PLoS – All journals (2008) PLoS – All journals (2009) PLoS – All journals (2010) PLoS – All journals (2011) PLoS – All journals (2012) PLoS – All journals (2013) PLoS Biology PLoS Computational Biology PLoS Genetics PLoS Medicine PLoS NTD PLoS Pathogens PLoS One
- 39. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 39 ANALYSES PLoS One – All years PLoS One (2008) PLoS One (2009) PLoS One (2010) PLoS One (2011) PLoS One (2012) PLoS One (2013)
- 40. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 40 ANALYSES PLoS One – All years PLoS One (2008) PLoS One (2009) PLoS One (2010) PLoS One (2011) PLoS One (2012) PLoS One (2013)
- 41. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 41 ANALYSES PLoS One – All years PLoS One (2008) PLoS One (2009) PLoS One (2010) PLoS One (2011) PLoS One (2012) PLoS One (2013)
- 42. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 42 ANALYSES PLoS One – All years PLoS One (2008) PLoS One (2009) PLoS One (2010) PLoS One (2011) PLoS One (2012) PLoS One (2013)
- 43. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 43 ANALYSES PLoS One – All years PLoS One (2008) PLoS One (2009) PLoS One (2010) PLoS One (2011) PLoS One (2012) PLoS One (2013)
- 44. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 44 ANALYSES PLoS One – All years PLoS One (2008) PLoS One (2009) PLoS One (2010) PLoS One (2011) PLoS One (2012) PLoS One (2013)
- 45. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 45 ANALYSES PLoS One (2007-2011) PLoS One (2008) PLoS One (2009) PLoS One (2010) PLoS One (2011) PLoS One (2012) PLoS One (2013)
- 46. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 46 ANALYSES 2007-2011 PLoS One PNAS JACS J Mat Chem Phys Rev Lett J Nanosci Nanotechn LNCS
- 47. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 47 ANALYSES 2007-2011 PLoS One PNAS JACS J Mat Chem Phys Rev Lett J Nanosci Nanotechn LNCS
- 48. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 48 ANALYSES 2007-2011 PLoS One PNAS JACS J Mat Chem Phys Rev Lett J Nanosci Nanotechn LNCS
- 49. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 49 ANALYSES 2007-2011 PLoS One PNAS JACS J Mat Chem Phys Rev Lett J Nanosci Nanotechn LNCS
- 50. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 50 ANALYSES 2007-2011 PLoS One PNAS JACS J Mat Chem Phys Rev Lett J Nanosci Nanotechn LNCS
- 51. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 51 ANALYSES 2007-2011 PLoS One PNAS JACS J Mat Chem Phys Rev Lett J Nanosci Nanotechn LNCS
- 52. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 52 ANALYSES 2007-2011 PLoS One PNAS JACS J Mat Chem Phys Rev Lett J Nanosci Nanotechn LNCS
- 53. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 53 SUMMARY Mapping the PLoS thesaurus directly (using co-occurrence) gave maps that were only partially useful. Indirect mapping of the PLoS thesaurus using a comprehensive map of the scientific literature (based on Scopus data) was very successful. The resulting visualization of the PLoS thesaurus became a stand-alone basemap, a template that can be used to: » Examine the thesaurus structure, content, and level of detail. » Show coverage and trends for various entities such as journals, institutions, authors, etc. This thesaurus mapping effort helped visualize which areas of the PLOS thesaurus were covered well, or not well enough, as well as which fields were emerging or well-established. All overlays based on tabular data, so detailed analysis is possible.
- 54. Physics Chemistry Engineering Biology Disease Medicine Brain Health Social Computer Patents 54 QUESTIONS Thank-you for your attention !