Google toolbar button to search Scirus (21-Apr-06)

Another toolbar button (these are peasy!):

Requirements as before i.e. Google Toolbar version 4 (beta), Internet Explorer.

- the Scirus seach button

• Uses the typed or selected text to search Elsevier's Scirus "For Scientific Information Only" search engine.
• Selecting and right-clicking any text in a webpage will show "Scirus" on the context menu as shown below. Clicking there will search Scirus with that text.
• Clicking the toolbar button without any search term will take you to www.scirus.com.

Images below the fold:

Google steals my bandwidth (21-Apr-06)

My genomics/bioinformatics custom buttons for the Google toolbar have graduated to the official button gallery:

http://toolbar.google.com/buttons/gallery?q=Zac+Hanley

Is this better than a mention on boingboing? Can't…tell…yet. Head…spinning. Too…much…fame…

Google Toolbar button to fetch US patents (12-Apr-06)

More toolbar hackery:

Requirements as before i.e. Google Toolbar version 4 (beta), Internet Explorer.

- the USPTO fetch-by-patent-number button

• Takes the typed or selected number and takes the user to the US patent with that number on the official US patent website. Numbers with or without commas are acceptable i.e. 7,027,987 or 7027987 both work.
• Selecting and right-clicking a number in a webpage will show "Fetch US patent by number" on the context menu as shown below. Clicking there will take the user to that patent on the USPTO website.
• Clicking the toolbar button without any search term will take you to www.uspto.gov/main/patents.htm.

Images below the fold:

Google Toolbar buttons for genomics and bioinformatics (07-Apr-06)

The fruits of more coding:

Requirements: Google Toolbar version 4 (beta), Internet Explorer.

- the Entrez search button

• Performs a search of Entrez, the combined NCBI-NLM life sciences search engine at NIH. Their database contains biomedical literature, gene and protein sequences, 3D biomolecular structures, genomes, SAGE tags, lots more.
• Selecting and right-clicking any word or phrase in a page (e.g. Arabidopsis, cytochrome) will show "Search Entrez at NCBI" on the context menu. Clicking there will search Entrez with the selected text.
• Clicking the toolbar button without any search term will take you to www.ncbi.nih.org/Entrez.

- the PubMed search button

• Performs a search of the PubMed biomedical citation database hosted at NCBI. PubMed contains several million of abstracts and bibliographic records of research papers published in thousands of journals around the world over the last forty years.
• Selecting and right-clicking any word or phrase in a page (e.g. succinyl CoA, Crick) will show "Search PubMed" on the context menu. Clicking there will search PubMed with the selected text.
• Clicking the toolbar button without any search term will take you to www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed (the main entry page).

- for completists, the DOI lookup button again

• Takes a DOI number e.g. 10.1038/35057062 and passes it to the DOI Proxy, which redirects seamlessly to the official version of that document on the internet. One common use is scientific articles in major journals - the DOI directs the browser to the authoritative version of the research work hosted on the journal's own website (even if the site has been redesigned or content relocated).
• Selecting and right-clicking a DOI in a page will show "Fetch Digital Object by DOI" on the context menu. Clicking there will direct you (via the DOI Proxy) to the authoritative document for that DOI.
• Clicking the toolbar button without any search term will take you to www.doi.org.

Google Toolbar DOI lookup button (06-Apr-06)

I've been coding. Let there be rife click-thru™!

Click to add my new button to the Google Toolbar on your browser. (Works in IE only. If you have an older version of the toolbar, or don't have it at all, Google will offer you version 4. If you have Firefox then grit your teeth and switch to IE for five minutes please.) It'll end up looking like this, only with better resolution (I only had Paint handy):

This new white-triangle-blue-circle button adds a new function: it performs an instant lookup for a DOI, those number codes that function as persistent URLs on many scientific papers and articles (and some other data objects). Pasting a DOI into the searchbox as in the picture and clicking the new button should push you straight to the official online version of that research paper.

An example: after install, cut and paste just the DOI from this citation (just the "XX.YYYY/ZZZZZZZZZ" bit) into the search box and try it.

You should be sent straight to the abstract on Nature's website. It works by sending a query through the DOI Proxy hosted by the Digital Object Identifier System (more background at Wikipedia). And if Nature redesigns their site structure - well, their (automatic) arrangement with the DOI folk updates the proxy and you are effortlessly sent where you expect to go. The other big publishers do the same, and many small ones. DOIs are designed to persist past and over site rearrangements.

But wait, there's more

We have non-evil smarttag-like functionality too! Select a DOI anywhere in webpage text in IE and right-click - a DOI lookup option should appear on the context menu. Here's one to try:

doi: 10.1371/journal.pgen.0020043

And here's what it should look like:

(If you get a different, shorter context menu then you might be getting interference from other toolbars. The MSN Search toolbar did this to me. Turn it off for the purposes of this demo with View…Toolbars. And ask Microsoft about the third and fourth of these software principles.)

Thanks to Google's Toolbar API, this trickery is jocularly trivial: it's just this XML file down in your C:\Documents and Settings\ tree on a PC (dunno about Macs). I will be setting up buttons and context menus for NCBI-Entrez and the USPTO and others shortly. And I'll be sending the DOI one to the DOI folks to (hopefully) put on their list of tools.

There's an Enterprise edition of the v4 toolbar too, for companies who see value in this but are used to more IT command-and-control.

Firefox and Google Base

None of this works in Firefox because custom buttons aren't yet available in the latest toolbar for that browser (v2) at this time. This could switch me back to IE… (In other words: hurry up, Google!)

And the XML file is here on ortholog because Google doesn't host it. If you look in the directory mentioned above, you'll see the file ends up named with a hashed version of www.ortholog.com. I tried hosting the code on my corner of Google Base--i.e. here--but that doesn't seem to work. Weird, cos it works with modules designed for Google Personalized Homepage such as my Google Scholar searchbox module. Perhaps I'm doing it wrong. Must ask them.

Google Scholar redux (23-Mar-06)

Google wouldn't let me put a Google Scholar search box hereabouts. Well, that's not strictly accurate: they wouldn't let me take the <TABLE> tags and border elements out so that the page would still be valid XHTML 1.0 Strict (or, as it more usually is, valid XHTML 1.0 Not-Counting-Ampersands-In-URLs). That seemed a little needless to me.

Well, things have changed. The Google Scholar searchbox terms of service have gone all complicated, and there are example modules for the Google Homepage that use the Google Fusion API and Google Base to add extra searchboxes. The goalposts have shifted. So I've become a programmer:

1. Take the modified searchbox HTML I wrote earlier
2. Wrap it in the module XML as specified in the API
3. Upload to Google Base
4. Add to my Google homepage

Here it is:

The code is at http://base.google.com/base/a/1040659/6208845733264550245. Try it:

No Google Scholar search box (25-May-05)

I wanted to take advantage of Google's offer of a search box for Google Scholar on the main page of my site. However, ortholog aspires to be valid XHTML 1.0 Strict since better living can be achieved that way. But the code that Google provides isn't standards-compliant. So I can't.

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Essential knowledge.