Launching the ScienceSeeker search API

ScienceSeeker API logo

Today, we are launching version 2.1 of ScienceSeeker. We have enhanced the site in many ways, but the big new feature is our new search API. You can use this tool to find anything in our database of over 1,000 blogs and 120,000 posts. We added a variety of options to let you sort by things like title, summary, number of recommendations, or even posts talking about a specific peer-reviewed article.

This release provides the foundation and most basic feature: search functionality. It can be used by developers interested in creating something using ScienceSeeker; we are planning to release a user interface for it shortly.

Here are some of examples of the things you can do with this new tool:

For more information about the search and filters, and how you can use them in your application or website, visit our API documentation page or contact us for questions and requests.

Searching ScienceSeeker blogs

ScienceSeeker is developing an API to allow other services to access
our database, and we’d like your input as we proceed. The details of
an API can be complex, but the concept is simple: It’s a way that
websites, applications, and other services can use our data to build
additional functionality. For example, a journal might want to show
its readers how frequently their articles are being cited by blogs,
and when our API is complete, they could use ScienceSeeker’s database
to find out.

The API consists of a single web request to the search application. All
search parameters will be contained within that request, as parameters
in the URL. The search application will return XML-encoded data which
will contain relevant search results.

You can search for blogs, for posts, or for topics. For example, you
might want to search for all blogs which contain “Skeptic” in the title,
or all posts with a topic of “Deep Sea Dive”. (You can’t search blogs
and posts at the same time; you have to select one type of object to
search.)

The supported list of search queries, or “filters,” is still in
development. We expect to support searching by title, topic, summary
text, citation, URL, posts to a blog with a specific title or topic, and
some other filters.

We are also in the process of developing a second means of accessing the
API, which would support more complicated queries with AND, OR, and NOT
syntax. For now, multiple filters in a query will be considered to be
“AND”ed together.

The documentation for the API is not solidified yet, but is available
for reading
. Feedback is welcome!

Introducing our new slate of editors

Here’s the slate of editors that will be offering their expert recommendations, selecting the best posts in their favorite fields of study. Each editor will choose 4 to 5 posts a week from among the hundreds we collect each day, making it easier for you to find the best posts on ScienceSeeker. You can also follow their picks on Twitter.

Sarah Chow
When not busy in the lab measuring the thermodynamic properties of the reaction between a molecule called cAMP and the Pacemaker protein, Sarah Chow spends a lot of her nights tweeting, blogging and—her newest endeavor—podcasting for Experimental Podcast and video blogging on her website. On Saturday nights, you can find Sarah putting girl guides and boy scouts to sleep as the leader in charge of the sleep over program at Science World British Columbia.

To keep her sanity, she runs for miles in the beautiful trails of Vancouver. She will be making her picks in anthropology, biology, chemistry, ecology / conservation, health, medicine, and philosophy.

Matthew Francis
Matthew Francis is a science writer and speaker specializing in physics, astronomy, and related fields. He is a former college professor, ex-planetarium director, occasional musician, and frequent wearer of jaunty hats. He blogs about science and science communication at Galileo’s Pendulum; he is also the physics and math editor at Double X Science and freelance physics/astronomy writer for Ars Technica. His writing has appeared at Wired Science, the Scientific American Guest Blog, Culture of Science, and the 365 Days of Astronomy podcast. Matthew will be making his picks in astronomy and physics.

Cristy Gelling
Cristy Gelling is a postdoctoral cell biologist at the University of Pittsburgh working on the human genetic disease alpha-1 antitrypsin deficiency using her favorite domesticated organism, bakers’ yeast. She writes articles for Bitesize Bio that she hopes are useful for other lab rats, she blogs about science and her last days in the lab at The Blobologist, and when she’s feeling motivated she harasses her friends in Pittsburgh into writing about science at Steel City Science. She’s either from Australia or from New Zealand, depending on who’s asking the question. She will be selecting posts on biology, chemistry, and academic life.

Jason Goldman
Jason Goldman is a doctoral student and avid blogger and editor. He blogs at Thoughtful Animal, has served as Psychology and Neuroscience Editor for Research Blogging, and was editor of The Open Laboratory 2010. He will be selecting posts on psychology and neuroscience.

Mark Hahnel
Mark Hahnel is a stem cell biologist and geneticist who is the force behind Science 3.0. He’s currently helping with the development of ScienceSeeker, and he is Project Manager for Figshare. He’ll be making his editor’s picks in biology and genetics.

Peter Krautzberger
Peter Krautzberger studied mathematics in Munich and Berlin and recently spent two years at the University of Michigan as a DFG postdoctoral fellow. He founded mathblogging.org, the math copy-cat of scienceblogging.org, as well boolesrings.org, a network of academic homepages using wordpress. He will be making his picks in the field of mathematics.

Andrew Watt
Andrew Watt is a PhD candidate at the University of Melbourne where he is investigating diagnostic measures for Alzheimer’s disease, and a few other neurodegenerative conditions. He has a background in genetics and psychology and has even dabbled in documentary film-making, although that was quite some time ago now.

For many years Andrew has had a, some would say unhealthy, fascination with the human brain. And in an effort to share his fascination he created A Hippo on Campus, a blog where he investigates contemporary research from the fields of neuropsychology, neurobiology, and beyond. He’ll be making his editor’s picks in medicine, neuroscience, and psychology.

Allie Wilkinson
Allie Wilkinson is a freelance science writer and multimedia specialist with a background in environmental studies and conservation biology. She also founded This Is What A Scientist Looks Like, an ongoing community photo project to challenge the stereotypical perception of a scientist. You can follow her on her blog Oh, For the Love of Science! and Twitter. Allie will be making her editor’s picks on biology, conservation, ecology, environmental sciences, evolution, marine biology, and geosciences.

Introducing… New features and new editors!

Today ScienceSeeker is launching a fleet of new features that we think will make ScienceSeeker your go-to site for everything about science online.

To see all the new features, you may need to clear the cache on your browser. Here’s what you’ll see:

Expert Recommendations. Most importantly, we have seven new editors who will be helping you find the very best items from the hundreds collected by ScienceSeeker every day. You can check out the most recent Editor’s Picks in the right sidebar of the main page, and by checking the “Editor’s Picks” box in our new Filters section, you can see only the posts that have been recommended by our editors.

Flexible Filters. Speaking of filters, the new Filters feature in the left sidebar will help you narrow down the massive list of items in our feed. If you only want to see posts about Physics, or citing peer-reviewed sources, here’s the place to look. More importantly, you can combine the filters, and generate your own RSS feed. Maybe you just want to see Editor’s Picks on Biology, Astrophysics, and Medicine. Now you can, and you can view them on-screen or have them delivered to your preferred RSS reader.

Make your Own Suggestions. Our editors will be selecting fantastic items from the ScienceSeeker feed, but you don’t have to listen to just them. You can add your own voice to the mix with your own recommendations. Registered users can login, then click on the star next to any entry to recommend it. You can leave a note explaining why you like the post, and soon we’ll have a way for your notes to be automatically posted to social media sites.

Better Photos. ScienceSeeker now not only collects entries and articles from scientists and science writers, it also displays photos picked by our editors. A new slide show on our main page shows the week’s best images in science.

Cite your Sources. If you’re a writer or a blogger, you can now use our “Generate Citation” tool to create references to peer-reviewed journal articles. The code created by our site can be pasted into your blog and is recognized by ScienceSeeker, ResearchBlogging, Zotero, EndNote, and many other services. If you already have an account at ResearchBlogging, you can create a citation here and have it recognized by both ResearchBlogging and ScienceSeeker (And as before, we’ll continue to recognize citations created in ResearchBlogging).

We’d love to hear what you think of these new features—as well as your ideas for new ones. Let us know in the comments section below!

ScienceSeeker Seeks Science-Savvy Editors

ScienceSeeker is now one year old, and we’ve made some great strides in the past year. But in the next year, we’re planning even more. We’re about to get a whole lot more interactive, and we need people manage all that interactivity.

With over 900 blogs and hundreds of posts indexed each day, ScienceSeeker can sometimes be rather overwhelming. To help visitors sort through all that information, we’ll be relying both on our readers and specialized volunteer editors. We expect this new functionality to be ready within a few weeks, so to prepare for it, we need to sign up editors now.

The primary job of the new editors will be to share their favorite ScienceSeeker posts. They’ll select five posts a week from blogs covering their areas of expertise, and readers will be able to view those posts on our site or subscribe to a feed of just the recommended posts. We expect this to take just a few minutes each day.

Qualifications:

  • An active online presence on a blog and / or social networking sites like Twitter, Google+, and FaceBook
  • We don’t require that our editors have PhDs, but the candidates we select will have demonstrated expertise via their blogging or other publication record.
  • Enthusiasm for science

If you’re interested in the job, please email dsmunger@gmail.com with a paragraph or two about why you would like to be an editor, and provide a link to 2 or 3 of your own online posts about science that you feel are especially good. Link your social media feeds and other relevant sites, if any. You may attach or link to a curriculum vitae.

Editors will be permanently listed on ScienceSeeker.org, so this position will make a great addition to your CV. We will select the new editors by February 1, 2012.

18 Jan 2012: Updated to indicate the editorships are volunteer positions.

Share ScienceSeeker with our new badges

If you like ScienceSeeker, I hope you’ll add one of these badges to your blog. It’s a great way to let your readers know about ScienceSeeker, which, in turn, should point more readers your way. To use the badges, just copy the code beneath the badge you like best and paste it into your blog’s sidebar (for most blogs, using a “text” widget will work fine).

I'm on ScienceSeeker-DNA

<a href="http://scienceseeker.org/"><img src="http://scienceseeker.org/wp-content/uploads/2011/02/sciseekdna.gif" alt="I&#039;m on ScienceSeeker-DNA" title="sciseekdna" width="146" height="44" /></a>

I'm on ScienceSeeker-Microscope

<a href="http://scienceseeker.org/"><img src="http://scienceseeker.org/wp-content/uploads/2011/02/sciseekmicro.gif" alt="I&#039;m on ScienceSeeker-Microscope" title="sciseekmicro" width="146" height="44" /></a>

I'm on ScienceSeeker-Telescope

<a href="http://scienceseeker.org"><img src="http://scienceseeker.org/wp-content/uploads/2011/02/sciseekscope.gif" alt="I&#039;m on ScienceSeeker-Telescope" title="sciseekscope" width="146" height="44" /></a>

If you have any other ideas for badges, or other ways you’d like to share ScienceSeeker with your readers, let us know in the comments.

Questions about ScienceSeeker? (Open forum)

Following the ScienceSeeker launch, I saw various questions about the site on Twitter. If you have questions, ask them here, and we will answer!

Some questions I can answer now: yes, there is a rudimentary API to let people access posts directly; I will post more about that later. Yes, we do want to make the code for the site re-usable by other communities, so it is not limited to science topics in theory (see the job listings — we are looking for someone to help usher the code through an open source release so that others can use it to set up similar sites about other topics).

What else do you want to know? Ask here.

Introducing ScienceSeeker

We’re pleased to announce the unveiling of the product of six months of planning and work by some very dedicated volunteers. ScienceSeeker (at, naturally, Scienceseeker.org) is a beta-level site; a work in progress, but we think it’s a very useful work even as it now stands. The project began as an extension of Science Blogging Aggregated, but quickly grew into an independent site.

The basic concept is simple: Find as many sources of regularly-updated science information as possible, and collect them all in one place. We believe that science blogs are currently the most robust and diverse source of science news, discussion, and commentary. They can offer a measured response to the myriads of self-promotional press releases that clutter newspapers and inboxes. Unfortunately, they are spread all about the internet, in dozens of blogging networks and hundreds, if not thousands, of independent science blogs. These blogs and networks aren’t organized by topic, which makes it difficult for someone looking for latest posts on, say, chemistry.

ScienceSeeker already catalogs over 400 blogs, and is set up so that anyone can add more blogs. Our editors will review any submission to make sure it’s really about science (and not spam), then approve it within 24 hours. Our aim is to be the most comprehensive and useful aggregator of science news, discussion, and commentary anywhere.

Take a look at the site and put it through its paces. We think you’ll agree that it’s one of the most useful and engaging science sites you’ve ever seen.

Click here to visit ScienceSeeker.

ScienceSeeker is an all-volunteer effort, and we intend to make it a formal, open-source project, allowing anyone to contribute enhancements. We have lots of ideas of what to do next, but we want to hear yours too. Feel free to offer suggestions in the comments.

ScienceSeeker needs YOU!

ScienceSeeker is an all-volunteer project, and it’s not finished yet! We are planning big things, but we can only do them with community support. We need both technical help to create the site, and editorial support to maintain quality.

If you’re interested in being an editor, please indicate your interest below or use the contact form to email us.

Our technical needs are more specific; the positions we need to fill are listed below. If you have technical questions, feel free to email jphekman@arborius.net (Jessica Hekman). She will be online during the conference and will try to answer all emails within a few hours (often within minutes).

* DB/MySQL geek

Review the SQL queries in our code base and tighten them up for speed and efficiency. Add indexes to the database to make it run faster. In general, be in charge the efficiency of the (MySQL) database.

* PHP programmer

Write PHP (mostly WordPress plugins) to add new functionality to ScienceSeeker, and to fix bugs. We can use multiple people in this position! Some knowledge of XML is useful but not essential.

* Release engineer

Set up a source code repository (probably subversion). Design and set up a better development environment (beta and live versions of the site). Chaperone an open source release of the code base.

* XML/XSL geek

Much of the behind the scenes work in ScienceSeeker is XML documents, and many of them are transformed to HTML via XSLT. Maintain the XSLT stylesheets and write new ones as needed. Extend the XML schemas (currently informal, but may be formalized in RELAX-NG or XSD if you prefer) to support more functionality as ScienceSeeker expands. This job may or may not overlap with the PHP programming job.

Crowdsourcing request: Help us create a list of blogs for v. 2.0

Update: Thanks to everyone for your help! We’ve finished updating the database. Look here for news on our launch on Saturday, January 15.

In just under three weeks, we’ll be unveiling the beta version of the next generation of this site.

The new site will work very differently from this one; it is a custom-created database that collects information from hundreds—and ultimately thousands of blogs. Users will easily be able to select just the topics they want, instead of seeing posts based on what network they are on. We want the beta site to be usable from day one, but to do that, we need some help.

I’ve created a Google Docs Spreadsheet for this purpose. Anyone can access the spreadsheet and make modifications. What we need are the name, URL, RSS address, and topic of each blog. What we have, in most cases, is just the URL. If everyone pitches in and visits 10 to 20 blogs, then we should be able to generate this information in a matter of days, if not hours.

Most of the blogs are listed on the Master Blog List (the first tab at the bottom of the spreadsheet). To start helping, just fill in the information in the space provided. If you figure out an automated way of doing this, you can reserve a block of blogs by typing your name in the designated column; then no one will duplicate your efforts.

The reason we need humans to do this is that we want the blogs to be classified by topic. We’ve generated a list of topics (on the last tab in the spreadsheet). When you visit a blog, figure out what topic from our list best describes the blog, and enter it in the space provided (most web browsers will display a drop-down menu to make this easy for you).

The other tabs are for blog networks that are a little more difficult to suss out; either there was no easy way for us to find a list of blogs, or there are non-science blogs mixed in with science blogs. So, we’ve given specific directions for what to do in each case.

FAQs

  • My Blog Isn’t Listed!
    Don’t worry! Either we’ve already got all the info we need (in the case of some blog networks) or you’re an independent blogger and you’ll be able to register your blog when the site launches. If you don’t think you’re in either of those camps, let us know in the comments below
  • None of the official topics apply to this blog
    Just pick the closest match. You can get more specific in the secondary topic
  • I don’t agree with your list of topics
    We had to start somewhere. The list will be easily modifiable in the future.
  • One of the listed blogs is not scientific
    Explain your objection in the Notes section on the spreadsheet
  • Someone has reserved a block of blogs for hours
    You can use File –> See revision history to see how recently an update was made. If it’s been more than an hour, feel free to delete their name, substitute yours, and work on that entry
  • There’s no drop-down menu of topics
    Try using a different browser. I’ve tested it on Safari and Firefox, but I can confirm it doesn’t work on Chrome for Mac.
  • What’s in it for me?
    Our eternal gratitude? Plus, if we see you at a conference, we’ll buy you a beer

Thanks again. Let us know if you have any other questions in the comments.

Here’s another link to the Google Docs Spreadsheet