UCSF Profiles

UCSF’s most extreme cross-campus collaborators

/ Anirvan Chatterjee

UCSF is spread all across San Francisco, with faculty members’ primary addresses spanning over a dozen zip codes. We know that geographical proximity helps collaboration, but some UCSF researchers are comfortably working with collaborators all across the university, regardless of campus.

I used UCSF Profiles data to look at researchers who have co-authored publications since 2017 with other people currently at UCSF who have primary addresses in a different zip code. I skipped publications with more than 6 total co-authors, since it’s less likely that any two co-authors collaborated directly. (See the example at the end of this post.)

I expected most of the top cross-campus collaborators to be from Epidemiology & Biostatistics, UCSF’s most internally collaborative department—but the list wasn’t as lopsided as I expected.

The list

  • Isabel Elaine Allen (Epidemiology & Biostatistics) has, since 2017, co-authored 6 qualifying papers with UCSF people spread across 8 other ZIP codes
  • Patricia O’Sullivan (Medicine) has, since 2017, co-authored 14 qualifying papers with UCSF people spread across 8 other ZIP codes
  • Martha Shumway (Psychiatry) has, since 2017, co-authored 7 qualifying papers with UCSF people spread across 6 other ZIP codes
  • Christine Ritchie (Medicine) has, since 2017, co-authored 8 qualifying papers with UCSF people spread across 6 other ZIP codes
  • Emily Finlayson (Surgery) has, since 2017, co-authored 4 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Patrick Yuan (Epidemiology & Biostatistics) has, since 2017, co-authored 3 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Jason Satterfield (Medicine) has, since 2017, co-authored 4 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Youngho Seo (Radiology) has, since 2017, co-authored 5 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Rebecca Sudore (Medicine) has, since 2017, co-authored 4 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Christy Boscardin (Medicine) has, since 2017, co-authored 7 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Gabriela Schmajuk (Medicine) has, since 2017, co-authored 7 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Jinoos Yazdany (Medicine) has, since 2017, co-authored 7 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Bridget O’Brien (Medicine) has, since 2017, co-authored 6 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Mary Whooley (Medicine) has, since 2017, co-authored 5 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Amber Bahorik (Psychiatry) has, since 2017, co-authored 10 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Derek Satre (Psychiatry) has, since 2017, co-authored 11 qualifying papers with UCSF people spread across 5 other ZIP codes
  • John Boscardin (Medicine) has, since 2017, co-authored 9 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Kirsten Bibbins-Domingo (Epidemiology & Biostatistics) has, since 2017, co-authored 10 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Michael Matthay (Medicine) has, since 2017, co-authored 11 qualifying papers with UCSF people spread across 5 other ZIP codes
  • Eric Vittinghoff (Epidemiology & Biostatistics) has, since 2017, co-authored 21 qualifying papers with UCSF people spread across 5 other ZIP codes

Extended example

  • A (in 94158) co-authors a paper with UCSF colleague B (in 94117) and non-UCSF person C
  • A co-authors another paper with UCSF colleagues D (in 94110) and E (in 94158, the same as A)
  • A co-authors one more paper with ten co-authors — which doesn’t qualify, because we only care about papers with 2-6 total co-authors
  • A has therefore co-authored 2 qualifying papers with UCSF people spread across 2 other ZIP codes.

Photo: Philip Leara, public domain


RNS SEO: How 52 research networking sites perform on Google, and what that tells us

/ Anirvan Chatterjee / 2 Comments

Research networking systems (RNS) like Vivo, Profiles, SciVal, and Pure are meant to be used — but often fail to be discoverable by real users because of poor search engine optimization (SEO).

That’s why we’re releasing RNS SEO 2015, the first-ever report describing how RNS performs in terms of real-world discoverability on Google.

Continue reading →

SEO for Research Networking: How to boost Profiles/VIVO traffic by an order of magnitude

/ Anirvan Chatterjee

"Redwoods" by Michael Balint (cc-by)

The UCSF Profiles team has increased site usage by over an order of magnitude since the site’s big campus-wide launch in 2010. This “growth hacking” cheat sheet distills the key lessons learned during that period, and can be applied to almost any research networking platform, including VIVO, Profiles, and home-grown solutions. Continue reading →

The 100 top researcher keywords at UCSF

/ Anirvan Chatterjee

I was looking to dig into some examples of collaboration patterns in different research areas, when I realized I didn’t even know the basics — what do UCSF researchers actually research?

UCSF Profiles uses PubMed data to extract MeSH keywords for every publication by every UCSF researcher in the system. We can use this to look at the most commonly used MeSH keywords across every researcher’s body of work. There are lots of caveats here (looking at all publications emphasizes past research interests over current ones; we’re not grouping related obscure MeSH terms with more popular ones; MeSH term assignment practices change over time; and this analysis ignores someone’s role as a first, middle, or last author). But this is certainly a start.

Here’s what I found, using the latest UCSF Profiles data:

  1. 98 researchers have HIV Infections in their top 5 MeSH keywords
  2. 53 researchers have Breast Neoplasms in their top 5 MeSH keywords
  3. 42 researchers have Magnetic Resonance Imaging in their top 5 MeSH keywords
  4. 39 researchers have Tomography, X-Ray Computed in their top 5 MeSH keywords
  5. 39 researchers have Brain Neoplasms in their top 5 MeSH keywords
  6. 37 researchers have Internship and Residency in their top 5 MeSH keywords
  7. 37 researchers have HIV-1 in their top 5 MeSH keywords
  8. 34 researchers have Alzheimer Disease in their top 5 MeSH keywords
  9. 33 researchers have Prostatic Neoplasms in their top 5 MeSH keywords
  10. 32 researchers have Saccharomyces cerevisiae in their top 5 MeSH keywords
  11. 31 researchers have Brain in their top 5 MeSH keywords
  12. 31 researchers have Anti-HIV Agents in their top 5 MeSH keywords
  13. 30 researchers have Neoplasms in their top 5 MeSH keywords
  14. 30 researchers have Smoking in their top 5 MeSH keywords
  15. 29 researchers have Diabetes Mellitus, Type 2 in their top 5 MeSH keywords
  16. 29 researchers have Asthma in their top 5 MeSH keywords
  17. 28 researchers have Stroke in their top 5 MeSH keywords
  18. 28 researchers have Sexual Behavior in their top 5 MeSH keywords
  19. 27 researchers have Myocardial Infarction in their top 5 MeSH keywords
  20. 27 researchers have Proteins in their top 5 MeSH keywords
  21. 26 researchers have Neurons in their top 5 MeSH keywords
  22. 26 researchers have Skin Neoplasms in their top 5 MeSH keywords
  23. 26 researchers have Antineoplastic Combined Chemotherapy Protocols in their top 5 MeSH keywords
  24. 25 researchers have Cognition Disorders in their top 5 MeSH keywords
  25. 25 researchers have Homosexuality, Male in their top 5 MeSH keywords
  26. 25 researchers have Emergency Service, Hospital in their top 5 MeSH keywords
  27. 25 researchers have Students, Medical in their top 5 MeSH keywords
  28. 24 researchers have Obesity in their top 5 MeSH keywords
  29. 24 researchers have Glioblastoma in their top 5 MeSH keywords
  30. 23 researchers have Epilepsy in their top 5 MeSH keywords
  31. 23 researchers have Pancreatic Neoplasms in their top 5 MeSH keywords
  32. 23 researchers have Dementia in their top 5 MeSH keywords
  33. 23 researchers have Liver Transplantation in their top 5 MeSH keywords
  34. 23 researchers have Hispanic Americans in their top 5 MeSH keywords
  35. 23 researchers have Education, Medical, Undergraduate in their top 5 MeSH keywords
  36. 22 researchers have Lung in their top 5 MeSH keywords
  37. 22 researchers have Genetic Predisposition to Disease in their top 5 MeSH keywords
  38. 22 researchers have Saccharomyces cerevisiae Proteins in their top 5 MeSH keywords
  39. 22 researchers have Lung Neoplasms in their top 5 MeSH keywords
  40. 22 researchers have Glioma in their top 5 MeSH keywords
  41. 21 researchers have Drosophila in their top 5 MeSH keywords
  42. 21 researchers have Mass Screening in their top 5 MeSH keywords
  43. 21 researchers have Heart Defects, Congenital in their top 5 MeSH keywords
  44. 21 researchers have Anti-Bacterial Agents in their top 5 MeSH keywords
  45. 21 researchers have Liver in their top 5 MeSH keywords
  46. 21 researchers have Polymorphism, Single Nucleotide in their top 5 MeSH keywords
  47. 21 researchers have Physician-Patient Relations in their top 5 MeSH keywords
  48. 21 researchers have Signal Transduction in their top 5 MeSH keywords
  49. 21 researchers have Primary Health Care in their top 5 MeSH keywords
  50. 21 researchers have Nerve Tissue Proteins in their top 5 MeSH keywords
  51. 21 researchers have Stem Cells in their top 5 MeSH keywords
  52. 21 researchers have Drosophila melanogaster in their top 5 MeSH keywords
  53. 20 researchers have Colorectal Neoplasms in their top 5 MeSH keywords
  54. 20 researchers have Stress Disorders, Post-Traumatic in their top 5 MeSH keywords
  55. 20 researchers have Calcium in their top 5 MeSH keywords
  56. 20 researchers have Health Services Accessibility in their top 5 MeSH keywords
  57. 20 researchers have Smoking Cessation in their top 5 MeSH keywords
  58. 20 researchers have Epithelial Cells in their top 5 MeSH keywords
  59. 20 researchers have Wounds and Injuries in their top 5 MeSH keywords
  60. 20 researchers have Drosophila Proteins in their top 5 MeSH keywords
  61. 20 researchers have Models, Molecular in their top 5 MeSH keywords
  62. 19 researchers have Magnetic Resonance Spectroscopy in their top 5 MeSH keywords
  63. 19 researchers have MicroRNAs in their top 5 MeSH keywords
  64. 19 researchers have Respiratory Distress Syndrome, Adult in their top 5 MeSH keywords
  65. 19 researchers have Curriculum in their top 5 MeSH keywords
  66. 19 researchers have Aging in their top 5 MeSH keywords
  67. 19 researchers have Embryonic Stem Cells in their top 5 MeSH keywords
  68. 19 researchers have Caenorhabditis elegans in their top 5 MeSH keywords
  69. 19 researchers have Kidney Transplantation in their top 5 MeSH keywords
  70. 18 researchers have Heart Failure in their top 5 MeSH keywords
  71. 18 researchers have Membrane Proteins in their top 5 MeSH keywords
  72. 18 researchers have Asian Americans in their top 5 MeSH keywords
  73. 18 researchers have DNA in their top 5 MeSH keywords
  74. 18 researchers have Tuberculosis in their top 5 MeSH keywords
  75. 18 researchers have Mental Disorders in their top 5 MeSH keywords
  76. 18 researchers have Transcription Factors in their top 5 MeSH keywords
  77. 18 researchers have Coronary Disease in their top 5 MeSH keywords
  78. 18 researchers have Gene Expression Profiling in their top 5 MeSH keywords
  79. 17 researchers have DNA-Binding Proteins in their top 5 MeSH keywords
  80. 17 researchers have CD8-Positive T-Lymphocytes in their top 5 MeSH keywords
  81. 17 researchers have Skin Diseases in their top 5 MeSH keywords
  82. 17 researchers have Bacterial Proteins in their top 5 MeSH keywords
  83. 17 researchers have Apoptosis in their top 5 MeSH keywords
  84. 17 researchers have Protein-Serine-Threonine Kinases in their top 5 MeSH keywords
  85. 17 researchers have Homeodomain Proteins in their top 5 MeSH keywords
  86. 17 researchers have Hypertension in their top 5 MeSH keywords
  87. 17 researchers have Stress, Psychological in their top 5 MeSH keywords
  88. 17 researchers have T-Lymphocytes in their top 5 MeSH keywords
  89. 17 researchers have Abortion, Induced in their top 5 MeSH keywords
  90. 17 researchers have Schizophrenia in their top 5 MeSH keywords
  91. 17 researchers have Antineoplastic Agents in their top 5 MeSH keywords
  92. 17 researchers have Proteomics in their top 5 MeSH keywords
  93. 17 researchers have Multiple Sclerosis in their top 5 MeSH keywords
  94. 17 researchers have Teaching in their top 5 MeSH keywords
  95. 17 researchers have Acquired Immunodeficiency Syndrome in their top 5 MeSH keywords
  96. 17 researchers have Hepatitis C in their top 5 MeSH keywords
  97. 17 researchers have Laparoscopy in their top 5 MeSH keywords
  98. 16 researchers have Muscle, Skeletal in their top 5 MeSH keywords
  99. 16 researchers have Amyloid beta-Peptides in their top 5 MeSH keywords
  100. 16 researchers have Ovarian Neoplasms in their top 5 MeSH keywords

Every researcher at UCSF — by department

/ Anirvan Chatterjee

Co-authorship networks can help us understand internal research collaboration patterns at UCSF. I used data from UCSF Profiles to create a visualization of (almost) every researcher currently at UCSF, and how their intra-UCSF co-authorship networks break out by department.

This visualization by department bears some more investigation than the previous one by school. Department of Medicine researchers are all over, collaborating with a wide variety of external departments. But an initial visual inspection suggests that almost all major departments have co-authorship relationships with members of other departments; some, like neurology, appear to form large standalone clusters, while others, like radiology, are more enmeshed in the work of others. This visualization flattens complex relationships into two dimensions, but it’s a starting point as we work to understand how UCSF collaborates.

View full-size visualization (PDF)

Every Researcher at UCSF, by department

Departmental BFFs: Which UCSF departments publish the most often together?

/ Anirvan Chatterjee

Batman and Robin smoking

Some UCSF departments work more closely together than others. I looked at co-authorship patterns in papers published between January 2012 and November 2013, based on data in UCSF Profiles, and pulled out the UCSF departments that collaborate the most frequently. The results aren’t necessarily surprising. The Department of Medicine is huge, and their cross-departmental collaborations make up 8 of the top 10 collaborations, measured by volume. On the flip side, smaller groups with research areas similar to others make up many of the most common collaborations, by percentage; for example, one-third of papers by researchers primarily affiliated with the Proctor Foundation for Research in Opthalmology are co-authored with researchers from the Department of Opthalmology. I wouldn’t have necessarily guessed, however, connections like that between nursing and psychiatry.

Top UCSF cross-departmental collaborations, by volume

  1. Epidemiology & Biostatistics + Medicine: 365 collaborative papers
  2. Medicine + Pediatrics: 139 collaborative papers
  3. Medicine + Psychiatry: 127 collaborative papers
  4. Neurological Surgery + Neurology: 115 collaborative papers
  5. Medicine + Pathology: 105 collaborative papers
  6. Laboratory Medicine + Medicine: 104 collaborative papers
  7. Medicine + Surgery: 99 collaborative papers
  8. Neurology + Radiology and Biomedical Imaging: 92 collaborative papers
  9. Medicine + Radiology and Biomedical Imaging: 90 collaborative papers
  10. Medicine + Neurology: 86 collaborative papers

Top UCSF cross-departmental collaborations, by percentage

  1. 64.8% of School of Nursing Dean’s Office papers are co-authored with Physiological Nursing
  2. 36.8% of Proctor Foundation papers are co-authored with Ophthalmology
  3. 33.8% of School of Nursing Dean’s Office papers are co-authored with Medicine
  4. 33.3% of Physiological Nursing papers are co-authored with School of Nursing Dean’s Office
  5. 33.3% of Institute for Neurodegenerative Disease papers are co-authored with Neurology
  6. 32.4% of School of Nursing Dean’s Office papers are co-authored with Psychiatry
  7. 29.8% of Physical Therapy & Rehab Sciences papers are co-authored with Radiology and Biomedical Imaging
  8. 27.5% of Physiological Nursing papers are co-authored with Medicine
  9. 25.0% of Epidemiology & Biostatistics papers are co-authored with Medicine
  10. 22.8% of Family & Community Medicine papers are co-authored with Medicine

Details: Data is drawn from UCSF Profiles, and is based on a list of all publications listed on PubMed published between Jan 2012–Nov 2013, focusing on those whose authors include groups of researchers that have primary affiliations to more than one UCSF department. We counted only those publications from researchers with a listed department, and for the purposes of counting top cross-departmental collaborations by percentage, only those collaborations that generated 10 or more papers during the time period. No attempt was made to account for the widely varying sizes and scopes of different departments, the fact that researchers may have multiple departmental affiliations, or the fact that some publications may have been authored before the researchers were affiliated with their current primary departments at UCSF.

Photo: “Glasgow’s own superheroes having a smoke outside the Counting House” by Stephen Fyfe/Flickr, under CC-BY-NC-ND

UCSF’s top 20 most diverse internally-collaborative departments

/ Anirvan Chatterjee

When UCSF researchers collaborate between departments, how diverse are the collaborations? Here are the top 20 UCSF departments, ranked by the average numbers of UCSF departments their multi-departmental papers include as co-authors (from among the 39 departments whose researchers had a total of 25+ multi-departmental publications published between January 2012 and November 2013).

Details: Data is drawn from UCSF Profiles, and is based on a list of all publications listed on PubMed published between Jan 2012–Nov 2013 whose authors include groups of researchers with primary affiliations to more than one UCSF department. We counted only those publications from researchers with a listed department, and only those departments whose current associated researchers published 25+ publications in conjunction with current members of other UCSF departments between Jan 2012–Nov 2013. No attempt was made to account for the widely varying sizes and scopes of different departments, the fact that researchers may have multiple departmental affiliations, or the fact that some publications may have been authored before the researchers were affiliated with their current primary departments at UCSF. These are the top 20 departments, out of a total of 39 that match our criteria.

  1. Physiological Nursing: co-authors from avg. 2.57 other UCSF departments, among 116 multi-department papers
  2. School of Nursing Dean’s Office: co-authors from avg. 2.44 other UCSF departments, among 52 multi-department papers
  3. Anesthesia/Perioperative Care: co-authors from avg. 1.84 other UCSF departments, among 69 multi-department papers
  4. Physiology: co-authors from avg. 1.83 other UCSF departments, among 29 multi-department papers
  5. Family Health Care Nursing: co-authors from avg. 1.64 other UCSF departments, among 47 multi-department papers
  6. Laboratory Medicine: co-authors from avg. 1.63 other UCSF departments, among 104 multi-department papers
  7. Pharmaceutical Chemistry: co-authors from avg. 1.63 other UCSF departments, among 120 multi-department papers
  8. Pathology: co-authors from avg. 1.62 other UCSF departments, among 234 multi-department papers
  9. Radiation Oncology: co-authors from avg. 1.60 other UCSF departments, among 53 multi-department papers
  10. Microbiology and Immunology: co-authors from avg. 1.57 other UCSF departments, among 49 multi-department papers
  11. Cellular & Molecular Pharmacology: co-authors from avg. 1.57 other UCSF departments, among 74 multi-department papers
  12. Orofacial Sciences: co-authors from avg. 1.57 other UCSF departments, among 53 multi-department papers
  13. HDF Comprehensive Cancer Center: co-authors from avg. 1.55 other UCSF departments, among 31 multi-department papers
  14. Anatomy: co-authors from avg. 1.55 other UCSF departments, among 55 multi-department papers
  15. Pediatrics: co-authors from avg. 1.53 other UCSF departments, among 321 multi-department papers
  16. School of Nursing Community Health Systems: co-authors from avg. 1.52 other UCSF departments, among 31 multi-department papers
  17. Surgery: co-authors from avg. 1.50 other UCSF departments, among 227 multi-department papers
  18. Biochemistry & Biophysics: co-authors from avg. 1.49 other UCSF departments, among 75 multi-department papers
  19. Neurological Surgery: co-authors from avg. 1.47 other UCSF departments, among 393 multi-department papers
  20. Cardiovascular Research Institute: co-authors from avg. 1.45 other UCSF departments, among 53 multi-department papers

UCSF collaborations, visualized

/ Anirvan Chatterjee

UCSF researchers often work closely with one another, across departments. We used data from UCSF Profiles to visualize how different departments work together, based on co-authorship patterns.

Visualization details: Data is drawn from UCSF Profiles, and includes all publications co-authored by current UCSF researchers from two more departments and listed on PubMed. The size of each department corresponds with the number of publications that members have published that include partnerships with other departments. The width of the lines connecting departments corresponds to the number of publications between two departments. Colors indicate clusters of departments that often publish collaboratively, based on network modularity. No scaling is done to account for varying sizes of different departments.

Click to view full-size image

UCSF internal collaborations, by department, based on publication co-authorship

Enhance your research networking platform, the UCSF way

/ Anirvan Chatterjee

Golden Gate Bridge

CTSI at UCSF has invested in increasing the usage and usability of UCSF Profiles, our research networking system. Based on our presentation at the 2012 IKFC meeting, here are our top 5 technical tips on how to increase the impact of your institution’s investment in research networking platforms, based on our past three years of work.

1. Measure

You can’t understand how you’re doing without measuring usage.

  • Install Google Analytics, then learn how to use this incredibly powerful tool (make sure to segment on-campus vs. off-campus traffic by setting up advanced segments based on service provider)
  • Register your site on Google Webmaster Tools to understand how search engines see your data

2. Optimize for search engines

UCSF Profiles gets over 50,000 visits a month. 72% of that traffic comes from search engines, primarily Google. Here’s how to increase traffic from search engines:

  • Implement a sitemap containing links to all your people profile pages, and make sure Google sees it using Google Webmaster Tools
  • Add a readable meta description (e.g. “Jane Doe’s profile, publications, research topics, and co-authors”) to your profile pages so they look better in search engine results
  • Add Schema.org data about your people on people profile pages
  • Advanced: use rel=canonical to prevent different versions of the same content from being indexed

3. Build inbound links

Linking is a critical way to both increase site traffic, and to signal importance to search engines.

  • Get websites large and small at your institution to link to your site (two years after launch, there are over 100 websites at UCSF that link to one or more pages on Profiles)
  • Encourage heavy linking to individual profile pages, e.g. from the campus directory, news articles, departmental profiles

4. Reuse data

Your research profiling system comes with APIs. Encouraging campus-wide reuse of this data can increase the impact of your investment. See opendata.profiles.ucsf.edu to see how UCSF is marketing this data.

  • Learn how to use your system’s APIs, so you can share that experience with others
  • Publicly document how the APIs work, and include sample source code
  • Reach out to campus technologists and webmasters to demonstrate how easy it is for them to reuse your data (e.g. the inclusion of Profiles data in UCSF’s mobile app was the result of technologist outreach)
  • Reach out to campus leaders to show them what kind of efficiencies they can gain by reusing your data (e.g. the inclusion of links to researcher profiles on the UCSF Directory was the result of a strategic partnership)

5. Extend with ORNG (advanced)

ORNG (OpenSocial Research Networking Gadgets) is a plugin system that allows you to add new apps into instances of Profiles or VIVO. Apps are written in HTML, CSS, and JavaScript, and are easy to share and reuse.

  • Install ORNG (OpenSocial) into your copy of Profiles or VIVO
  • Add new apps from the ORNG library of free apps
  • Write your own apps — most JavaScript programmers can get started in hours

Good luck! Feel free to leave comments and questions on this post—we’re happy to share what we know.

P.S. Thinking about how to make your campus equipment/services more discoverable? Try UCSF’s Plumage, the open source platform behind UCSF Cores Search.

Photo credit: digitonin via photopin cc