Help / Frequently asked questions
What is PombeTree?
The Academic Genealogy of Fission Yeast Genetics is a free, volunteer-run website designed to help you track your academic genealogy. Our goal is to collect information about the graduate student and postdoctoral relationships between most researchers in the field. This tree exists as a part of the larger Academic Family Tree, which seeks to build a genealogy across multiple academic fields.
What's new on PombeTree?
You might notice that the appears of the site has changed. We've updated the interface in an attempt to make it more attractive and easier to use. We're also working methods for linking researchers in the tree to their publications. We have also started experimenting with methods for measuring similarity between researchers based on the content of their publications, accurate inasmuch as publications are properly assigned to their authors. This information is currently overlaid on the tree display in the beta test site.
Unfortunately, along the way, it's possible that an occasional bug or confusing feature has been introduced. If you notice anything that needs to be fixed or improved, please report bug/errors here. And keep an eye out for further improvements down the road!
These updates are possible thanks to a grant from the Metaknowledge Network.
How do I navigate the tree?
There are several ways to wander around PombeTree. The basics are summed up in the commands at the top of each page:
- Tree - Jump to a random node on the tree
- Search - Search for a specific person or people at a specific institution
- Recent additions - List the most recent additions
- Distance - Trace the connection between two people in the tree
- Add person - Add a new person to the tree (and be a good citizen!). You must sign up for an account to make additions.
Where does the information on this site come from?
Data in the tree is provided largely by visitors to the site (like you!). A group of volunteer editors works to keep the data accurate, and we hope all contributors will do the same. Contact the site administrator if you're interested in helping out with editing.
How can I contribute?
The Academic Family Tree is volunteer-run and not-for-profit. However, it costs money to keep the site and its associated database running. Your support is critical! Any size donation is welcome. If you donate $50 US or more, we will send you a nicely formated PDF of the family tree of a researcher of your choice! Learn more here:
In addition to financial support, we are always looking for collaborators to help with coding, analysis and visualization. If you have any questions about support, financial or effort, please contact admin at neurotree dot org.
How do I add new information?
Sign up for an account by clicking "Sign In/Register" in the upper right corner of the page. Once registered, you will be able to add and edit information to the site. To add a new person, click "New Person" on the top naviation bar. To add a new connection to an existing person, navigate to their info page and click "New Child" or "New Parent". First and last name are required for new people, and connections between two people require specifying the type of relationship (graduate student, postdoc, etc.). Any other details that can be provided are much appreciated, including instituional affiliations, research area keywords, years of training, and other biographical data.
How do I sign up?
Click here to sign up for a new account. You will have to provide a username and a password. This will give you permission to add new information.
How do I edit my information?
After you sign up for an account, you will be able to link your account to your own node, even if it was already entered by another user. If you skipped the account linking step during the initial sign-up, you can take care of it by clicking on "My node" at the bottom of the page after logging in.
Why isn't there a tree for my field?
Because you haven't started one yet! It's easy. This tree is just one in the Academic Tree project. Just send us an email and we'll tell you what's involved in setting up a tree that focuses on your field of research.
What if I find a mistake?
Try to fix it yourself. Once users are logged in, they can edit their own tree entry as well as any other entries they have made. We protect other entries from editing to prevent vandalism. If you can't fix the error yourself, you can click on a "report error" link and send us an email with the relevant info. Alternatively, if you'd like to fix errors yourself, you can request to be a site editor.
How do I become a site editor?
We'd love to have your help! Send an email to forsburg at usc.edu asking for editor privileges for your account. This will allow you to edit all the existing entries on the site and help us manage error reports submitted by other users.
Can I print out a tree that looks nice?
Print quality varies with browsers. We have had decent luck with Firefox. Hopefully someday we will develop a cleaner system for printing. In the mean time, this is what works best:
- Click to the desired tree page
- Choose the smallest size from the display options.
- Go to the browser page setup/print options window and choose a) landscape, b) shrink page to fit, c) margins as small as possible and d) print background colors and images
- Try printing. If you want to get rid of the headers, print to a pdf and edit them out.
How do I report a bug or recommend an improvement for the site?
Please submit an error report or send an email to forsburg at usc.edu.
Who owns the data in the tree?
The data are owned by academictree.org, but they are shared under the Creative Commons License (CC-BY 3.0). You may use the data in the tree however you want, as long as you attribute the source, academictree.org.
What about privacy?
We have no interest in annoying or taking advantage of users who have generously donated their time to this effort. To that end, we will not share personal information (i.e., email addresses) with any commercial interests. The information that is displayed (name, institutional affiliation, home page, photo, mentor, etc.) is presumed to already be public knowledge. However, if you wish to have any information about you removed from the site, contact the administrator (forsburg at usc.edu), and we will respond promptly.
How can I export tree data for my own analysis?
Registered users should contact the site administator (admin at neurotree dot org) for instructions on how to export data from the tree database.
How do you identify researchers' publications?
Publications data are drawn from two databases: Medline and Scopus. Because of the large number of researchers with the same name, a disambiguation algorithm is required to accurately link researchers to papers they have authored. We match authors to papers using a two-step process. First, we identify candidate publications based on a simple string match between researcher name and the author list. Second, we look for overlap between co-authors and other individuals in the researcher's mentor network (trainees, mentors, collaborators, etc), and label publications with overlap as high-probability matches. Thus a complete family tree is likely to produce more accurate publication matches.
How do you measure similarity between researchers?
Latent semantic analysis is used to describe each publication abstract as a vector in a 400-dimensional space. Reseacher similarity is then measured by the distance between the average publication vector for each researcher.
How do you calculate "mean distance"?
where d(a,b) is the number of steps between people a and b. Averaging the inverse distance allows us to include unlinked people (d(a,b)=infinity) in the calculation. An analysis of mean distance for the whole tree can be found here.
Who is user "pq"?
Since 2001, the ProQuest dissertation database has documented the advisor associated with each doctoral dissertation in their system. We used this data to populate a large number of nodes in the system, and these additions are labeled as having been made by user "pq". Trainees and mentors for existing Academic Tree data were filled in based on name and institutional affiliation matches to the ProQuest data. We tried to be conservative and make only high-confidence matches to existing data, but there are likely to be some errors. If you do notice an error by pq, please don't get angry, but please do file an error report.
Can PombeTree tell me my Erdos number?
No. The Erdos number is based on coauthored publications. Links in this tree are based on mentorship relationships. These include graduate students, research assistants, and post-docs. Although students and their mentors often co-publish, there is not a strict relationship between the two. If you are interested in calculating your Erdos number, a good place to begin is here: http://www-users.med.cornell.edu/~jdvicto/erdos.html.
Are there other sites or resources like this?
PombeTree represents one discipline in the larger Academic Family Tree. If we are missing a tree for your field, you are welcome to start one! Please contact us at forsburg at usc.edu to learn more.
Elsewhere on the internet, we have located some similar projects, both large and small:
- The Mathematics Genealogy Project (a big one)
- Family Tree of Trade Economists (more focused but thorough)
- Brown University planetary geology family tree (a smaller one)
- Here's a diagram of relations between participants in the 2001 Cold Spring Harbor course on computational vision (contributed by Tony Movshon).
If you know of any other relevant links, let us know, and we'll add them to the list!