1 Topic by iain

  • iain
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Topic: species dictionaries

Hi

Are there any publically accessible species dictionaries which can be easily pruned into a format suitable for entry into Indicia so that I can supply the taxon, common name, authority, tvk (for example) to the warehouse. At the minute I'm pinching them from the NBN pages by expanding the various families and using the lower taxa of groups to produce a list, but that really is too much like hard work, even when using a wee bit of c#.

And as a follow on, is there any longer terms plans to have a sort of central repository of lists which can be accessed so that data entry for species is kept up to date and easily synchronised for warehouses?

Ta

Iain

2 Reply by Jim Bacon

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Re: species dictionaries

Hi Iain,

The central list is the UK Species Inventory managed by the Natural History Museum. They are working away at that with much encouragement from BRC and the NBN.

In the meantime, BRC have a database from which fairly decent species lists can be extracted should we receive a request from a collaborating organisation.

And, to turn your question on its head, should you start gathering records on your own warehouse, do you have a mechanism in mind to make them publicly accessible or available to a central repository (the NBN I am thinking of, naturally).

Jim Bacon.

3 Reply by iain

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Re: species dictionaries

Hi Jim

Yup, I did find that page but there didn't seem to be anything available for download there - I'll have another check, maybe I just missed the obvious...

I've only actually used the warehouse for my own records up until now as I've been struggling to find any free time to work on the interface to make it a bit more 'robust'. It's always been my intention to put the warehouse records onto NBN, but I was thinking in the longer term of some automated process which moves the data over some sort of web service rather than the usual export/import mechanism. But for now (or at least when there are sufficient records) I'll export them as usual with a global thingy (to be decided).

It'll be quite interesting, as the Mammal Survey records will go to NESBReC and so what'll likely happen is that a marked copy will go to NESBReC and then onto NBN, but these should all show as copies rather than the master record, and in theory all the warehouse records can also go to NBN as marked copies into other datasets. Presumably distinct records can then be sorted out using the global thingy prior to whatever use the download request was made for.

Hope that all makes some sort of sense

Ta

Iain

4 Reply by Jim Bacon

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Re: species dictionaries

Hi Iain,

Sorry, been away for a few days - up in your patch, in fact.

There is nothing to download from the NHM site as far as I am aware but you could ask for help on the Species Dictionary section of this forum which would put you in touch with Chris Raper who manages the inventory.

Alternatively you could try the NBN Species List web service

You clearly have similar ideas to us about exporting records. We, too, have been thinking about an automated process for getting records to the Gateway and I think the Gateway team will have been thinking about some automated way to receive them. I'm not informed about the current plan but make sure you keep in touch with us about that.

Also, with regard to exporting with a global thingy, which we have talked about before, it would be terribly good to ensure we all do that the same way.

Jim Bacon

5 Reply by andy_f

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Re: species dictionaries

Hello

As part of scoping out online recording tools I've been experimenting with Indicia.  The general aim is to have some fairly simple forms for use by staff within our Wildlife Trust to enter records which are then exported to our main Recorder database.

I initially decided to set up my own Indicia warehouse as I have access to a suitable server to run it off. However, having got it up and running without too much trouble I've hit a similar snag to Iain in finding a convenient way to populating species lists - whilst it would be fine to create my own .CSVs manually to upload for a small number of species for very species-specific surveys, one of the survey forms I'd like to create would be for very general casual records.

Having read this page about importing UKSI into Indicia I contacted NHM about the possibility of obtaining a copy. However I was also interested to note Jim's comment about NBN database from which a suitable list could be exported, and wonder what the chances of getting hold of this would be (if that would be a recommended way forward)?

The species list issue was not something I'd actually considered in advance, so this thread might serve as a useful heads up to anyone else with similar ideas of setting up their own warehouse.  Am now starting to think that requesting use of the BRC warehouse might have been a better idea after all...

Andy

6 Reply by johnvanbreda

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Re: species dictionaries

Hi Andy
I'm just about to run some final tests on an UKSI import here, so if you can wait a week or two I can provide the working setup.

Or, if you want to get cracking but accept there might be an occasional glitch in the species setup, I can send you the files to import as they stand now?

Cheers
John

John van Breda
Biodiverse IT

johnvanbreda's Website

7 Reply by iain

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Re: species dictionaries

Hi John

I'd be interested in that as well, can they be put into the upload area on the forum?

Ta

Iain

8 Reply by andy_f

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Re: species dictionaries

Hi John

Thanks very much for your response. It would be great if you could send the working setup - no problem waiting a week or two as I'm still testing out and familiarising myself with both warehouse and Indicia Instant. I'd also be interested in current version just to have a play around with in the meantime - though no problem if this is too much trouble to be worth it.


Thanks again.
Andy.

9 Reply by Jim Bacon

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Re: species dictionaries

Hi

Just adding a couple of notes here about work John has done while tidying up my inbox, not that I actually have any grasp on it.
1. There is some documentation on Importing the UKSI in to Indicia
2. There is a script in the code repository

I have set up a server to allow John to test this out but I think he is still to give it a go so I would advise everyone to wait for him to try it first.

Jim