Flags and Lollipops

Monday, October 08, 2007

Connotea & Postgenomic complaints

I was catching up on my Bloglines subscriptions and came across Tiageo's 'Pissed with Connotea' post about some complaints he had about some NPG products. I was going to reply in a comment but figured that T's points are worth addressing here, too.


1. [Connotea] Performance and downtime: Sometimes to submit a citation takes ages, or the service is down (although, regarding downtime, it seems to be getting better).


Yeah. This is something that has plagued Connotea recently though it is getting better as you say. Unfortunately the solutions aren't as easy as you might think. Ian Mulvany - who runs the site - was saying earlier that they're looking at adding a new server this week, which should help.


2. Postgenomic: When I tried to use it, it was mostly down. Want anedoctical evidence? If you search now (as of the posting date of this entry) for postgenomic on google, the cached page says: “Unable to select database”, nothing more.
3. Postgenomic again: A few months I submitted my blog. I got no answer at all.


These are also fair enough but I should point out that Postgenomic isn't an NPG product - it's run by me. NPG do let me keep developing it during work hours.

What I'm saying is - don't blame NPG, blame me. ;)

Downtime hasn't been a problem for Postgenomic recently, I don't think (I check it every day and it has been fine) but there *was* a long standing issue to do with firewalls and TCP/IP expiry timestamps that I won't bore you with - suffice to say that it meant that pages wouldn't load correctly on some platforms and that it's fixed now.

I know about the Google thing. It's a bit embarrassing but I haven't gotten round to doing anything about it yet..

re: not replying to your email... I'm normally quite good at getting back to people quickly (no, really). I found yours again and my excuse is that I was on a plane to SFO when I read it - must have put it on the 'to do' pile and forgotten about it. Sorry. :(

As a side note you're listed now.

HTH.

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Comments and trackbacks Feel free to post your comments Blogger Tiago Blogger Stew Anonymous maxine Anonymous Pawel Blogger Stew Blogger Bill Hooker . This post has trackbacks.

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6 Comments:

At October 08, 2007 11:11 AM, Blogger Tiago said...

Many thanks for the very fast answer. There is nothing better than seeing fast feedback to potential problems.

As I said in my post, I am a Connotea user, and really, my bibliographic database is (still) Connotea. But, the problem that I raise about incomplete DOI entries is quite serious, it simply means that manual work has to be done after bookmarking an article even with a DOI (check if journal and authors are there for instance). The truth is, JabRef (I am a bibtex user with JabRef on the top) is able to import PubMed entries (and others) from the web with 0 problems. I am thinking in going back to JabRef because I can't be bothered in completing something an automated system should be doing from me.

It would be great if somebody could tackle this problem.

Again, many thanks for the fast feedback.

 
At October 08, 2007 11:52 AM, Blogger Stew said...

Will email you directly about this.

We're hooked up directly to the CrossRef database so in theory whatever you see in Connotea is what the publisher of the article has associated with it...

(not doubting that there's a problem, though)

 
At October 08, 2007 9:22 PM, Anonymous maxine said...

Postgenomic has been fine the last three or four times I looked at it (last week).

 
At October 09, 2007 1:52 PM, Anonymous Pawel said...

There's one more small issue of Postgenomic server - the newest blog feed is not updating (according to that feed, Twisted Bacteria was the latest addition). Tiago's blog wasn't included. Is it a bug, or a feature?

 
At October 09, 2007 1:54 PM, Blogger Stew said...

Bit of both. ;) New blogs only appear in the index once a week (it's to do with the work involved behind the scenes calculating statistics, fetching Technorati portraits etc and is a bit broken). This'll change in later versions of Postgenomic.

 
At October 11, 2007 12:23 AM, Blogger Bill Hooker said...

I only have one Connotea complaint, but it keeps me from using the service -- duplicates. Until Connotea knows how to recognize the same paper added from the PubMed record and from the publisher's site (and wherever else), it's really sorta crippled for my purposes.

I know it's a difficult problem to automate, but I think it would be manageable if Connotea just took a stab at it -- a button for "here are papers with very similar author lists, now cull the dupes yourself miserable human".

(I know Ian et al are aware of the issue -- no doubt they have already put a fix in place and I'm about to look a tremendous idiot...)

 

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