Some VIVO Info Things

Visualizations, inspectors, reports, documents coming from your VIVO.

OpenVIVO data for your tools

OpenVIVO is an open VIVO that everyone can use. Hosted by Duraspace, Anyone can create a profile on OpenVIVO using their ORCiD. OpenVIVO exports its data every hour to an open text-based web site, where anyone can freely download all the data in the system at any time. Are you thinking of writing software to use VIVO data? To write VIVO data? Do you need to see or have a bunch of VIVO data for your work? No problem. Just download the OpenVIVO data and use it. Open VIVO Data

Organization Charts (using R) from VIVO

R is a popular, free software environment for statistical computing and graphics. R and VIVO were made for each other. R can readily issue queries to VIVO, returning data sets ready for data analytics and visualization. R has a learning curve, but many data analysts, and statisticians use R routinely, so finding someone with R experience is not difficult. Using R, we can treat the organizational structure of an institution as a network visualization problem - there is a "head node" (the university) and it has "child nodes" (organizations that report to the top level) and each in turn has its own sub-structure. VIVO represents organizational structure using a single predicate "obo:BFO_0000051" (has part). So in VIVO, we say The College of Medicine "has part" The Department of Surgery. These simple statements are used to represent the entire organizational structure. Using R, we can then visualize the structure using network representations. These non-traditional depictions are straightforward to make and highly informative. Download

NIH Biosketch from VIVO

Since the NIH VIVO project began in 2009, people have asked "Can VIVO make my NIH biosketch?" Now, perhaps, the answer is "yes." We've written software that makes a provisional biosketch solely from a person's URI in VIVO. The biosketch is produced in RTF, so that it can be hand-edited in Microsoft Word for inclusion in an NIH proposal submission. Hand editing is important -- faculty often want specific publications, grants or other accomplishments listed and others excluded. The software is under development. Additional features will be added as we go. But the power of VIVO is on full display here -- a complete biosketch is produced from a single URI, the format is absolutely controlled -- all biosketches produced from VIVO will be precisely and identically formatted, papers, grants and positions are included using rules -- no position, paper or grant is overlooked. Of course, the biosketch from VIVO is only as good as the data you have in VIVO. Download

Pilot Award Report in RTF

Reports from VIVO? Sure! Our Clinical and Translational Science Institute (CTSI) needed to have a report sowing the papers and grants that resulted from CTSI pilot award funding. They prepared a list of the investigators by year. A simple python program reads the list, looks up the papers and grants for each investigator that were obtained or published in the year of or after the year of the pilot award. All grants and papers are listed on the report. Investigators can then be asked "which of these papers or grants resulted from CTSI pilot award funding?" The report is a Rich Text Format File (RTF), a format developed by Microsoft that can be edited in Microsoft Word. RTF is very useful -- it is easy produced from Python, and easily edited by the people who will use the report -- a best of both worlds.Download

VIVO Triple Inspector

Inspector Form


Inspector Results


The VIVO Triple Inspector is for data managers who want to get as deep as possible with the data stored in VIVO. As you know, VIVO stores everything in a triple, subject, predicate, object. The Triple Inspector is a very simple tool -- given the URI of a subject in VIVO, show all the triples with that subject. The Triple Inspector is written in D3, a powerful JavaScript visualization library. You can try it here. Or Download

RSS Feeds

Consider making an RSS feed from data in your VIVO. At UF, we had several people ask us if we could recent published papers by UF faculty. Sure! A simple python program does a SPARQL query to identify recent papers -- papers published in the last 90 days, and added to VIVO in the last 14 days. The program then generates an XML file in RSS format. The XML file is placed on a web site where RSS readers can use it. And we imbed the RSS feed in web pages to display the feed using our normal web styles. View the feed imbedded in a web page here, subscribe to the RSS feed here, or Download

Sample SPARQL Queries

SPARQL is a great tool for technical people wishing to get information from VIVO. SPARQL is simple, powerful and comprehensive -- using SPARQL one can get just about any information in VIVO out of VIVO. Experienced data analysts can begin using SPARQL in one day. Excellent on-line resources are available. On this site we provide sample SPARQL queries for every occasion -- reports, lists and counts of papers, grants, people, and organizations. Modify these examples for your use. Sample SPARQL »