[API-users] Is there any NEO4J or graph-based driver for this API ?

Juan M. Escamilla Molgora j.escamillamolgora at lancaster.ac.uk
Tue May 31 22:08:43 CEST 2016


Hi Tim,

Thank you! specially for the DwC-A hint.

The cells are by default in decimal degrees, (wgs84 ) but the functions 
for generating them are general enough to use any projection supported 
by gdal using postgis. It could be done "on the fly" or stored on the 
server side,

I was thinking (day dreaming) in a standard way for coding unique but 
universal grids (similar to geohash or open location code), but didn't 
find something fast and ready. Maybe later :)

I only use Open Source Software, Python, Django, GDAL, Numpy, Postgis, 
Conda, Py2Neo, ete2 among others.

Currently I don't have an official release and the project is quite 
inmature, unstable as well as the installation could be non trivial.  
I'm fixing all these issues but will take some time,sorry for this.

The github repository is:

https://github.com/molgor/biospytial.git

An there's a very old documentation here:

http://test.holobio.me/modules/gbif_taxonomy_class.html

Please feel free to follow!


Best wishes


Juan

P.s. The functions for generating the grid are in: biospytial/SQL_functions





On 31/05/16 19:47, Tim Robertson wrote:
> Thanks Juan
>
> You're quite right - you need the DwC-A download format to get those IDs.
>
> Are the cells decimal degrees, and then partitioned into smaller 
> units, or equal area cells or maybe UTM grids or something else 
> perhaps? I am just curious.
>
> Are you developing this as OSS? I'd like to follow progress if possible?
>
> Thanks,
> Tim,
>
> On 31 May 2016, at 20:31, Juan M. Escamilla Molgora 
> <j.escamillamolgora at lancaster.ac.uk 
> <mailto:j.escamillamolgora at lancaster.ac.uk>> wrote:
>
>> Hi Tim,
>>
>> The grid is made by selecting a square area and divide it in nxn 
>> subsquares which form a partition on the bigger square.
>>
>> Each grid is a table in postgis and there's a mapping between this 
>> table to a django model (class).
>>
>> The class constructor have attributes: id, cell and neighbours (next 
>> release).
>>
>> The cell is a polygon (square) and with geodjango inherits the 
>> properties of the osgeo module for polygons.
>>
>> I've tried to use the CSV data (downloaded as a CSV request ) but I 
>> couldn't find a way to obtain the global id's for each taxonomic 
>> level (idspecies, idgenus, idfamily, etc).
>>
>> Do you know a way for obtaining these fields?
>>
>>
>> Thank you for your email and best wishes,
>>
>>
>> Juan
>>
>>
>> On 31/05/16 19:03, Tim Robertson wrote:
>>> Hi Juan
>>>
>>> That sounds like a fun project!
>>>
>>> Can you please describe your grid / cells?
>>>
>>> Most likely your best bet will be to use the download API (as CSV 
>>> data) and ingest that. The other APIs will likely hit limits (e.g. 
>>> You can't page through indefinitely).
>>>
>>> Thanks,
>>> Tim
>>>
>>> On 31 May 2016, at 18:55, Juan M. Escamilla Molgora 
>>> <j.escamillamolgora at lancaster.ac.uk> wrote:
>>>
>>>> Dear all,
>>>>
>>>>
>>>> Thank you very much for your valuable feedback!
>>>>
>>>>
>>>> I'll explain a bit what I'm doing just to clarify, sorry if this 
>>>> spam to some.
>>>>
>>>>
>>>> I want to build a model for species assemblages based on 
>>>> co-occurrence of taxa within an arbitrary area. I'm building a 2D 
>>>> lattice in which for each cell I'm collapsing the data into a 
>>>> taxonomic tree (the occurrences). For doing this I need first to 
>>>> obtain the data from the gbif api and later, based on the ids (or 
>>>> names) of each taxonomic level (from kingdom to occurrence) build a 
>>>> tree coupled to each cell.
>>>>
>>>>
>>>> The implementation is done with postgresql (postgis) for storing 
>>>> the raw gbif data and neo4j for storing the relation
>>>>
>>>> "Being a member of the [ specie, genus, family,,,] [name/id]" The 
>>>> idea is to include data from different sources similar to the 
>>>> project Matthew and Jennifer had mentioned (which I'm very 
>>>> interested and like to hear more) and traverse the network looking 
>>>> for significant merged information.
>>>>
>>>>
>>>> One of the immediate problems I've found is to import big chunks of 
>>>> the gbif data into my specification. Thanks to this thread I've 
>>>> found the tools that are the most used by the community 
>>>> (pygbif,rgbif, and python-dwca-reader). I was using urlib2 and 
>>>> things like that.
>>>>
>>>> I'll be happy to share any code or ideas with the people interested.
>>>>
>>>>
>>>> Btw, I've checked the tinkerpop project which uses the Gremlin 
>>>> traversal language as independent from the DBMS.
>>>>
>>>> Perhaps it's possible to use it with spark and Guoda as well?
>>>>
>>>>
>>>>
>>>> Does GOuda is working now?
>>>>
>>>>
>>>> Best wishes
>>>>
>>>>
>>>> Juan.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 31/05/16 17:02, Collins, Matthew wrote:
>>>>>
>>>>> Jorrit pointed out this thread to us at iDigBio. Downloading and 
>>>>> importing data into a relational database will work great, 
>>>>> especially if as Jan said you can cut the data size down to a 
>>>>> reasonable amount.
>>>>>
>>>>>
>>>>> Another approach we've been working on in a collaboration called 
>>>>> GUODA [1] is to build an Apache Spark environment with 
>>>>> pre-formatted data frames with common data sets in them for 
>>>>> researchers to use. This approach would offer a remote service 
>>>>> where you could write arbitrary Spark code, probably in Jupyter 
>>>>> notebooks, to iterate over data. Spark does a lot of cool stuff 
>>>>> including GraphX which might be of interest. This is definitely 
>>>>> pre-alpha at this point and if anyone is interested, I'd like to 
>>>>> hear your thoughts. I'll also be at SPNHC talking about this.
>>>>>
>>>>>
>>>>> One thing we've found in working on this is that importing data 
>>>>> into a structured data format isn't always easy. If you only want 
>>>>> a few columns, it'll be fine. But getting the data typing, format 
>>>>> standardization, and column name syntax of the whole width of an 
>>>>> iDigBio record right requires some code. I looked to see if 
>>>>> EcoData Retriever [2] had a GBIF data source and they have an 
>>>>> eBird one that perhaps you might find useful as a starting point 
>>>>> if you wanted to try to use someone else's code to download and 
>>>>> import data.
>>>>>
>>>>>
>>>>> For other data structures like BHL, we're kind of making stuff up 
>>>>> since we're packaging a relational structure and not something 
>>>>> nearly as flat as GBIF and DWC stuff.
>>>>>
>>>>>
>>>>> [1] http://guoda.bio/​
>>>>>
>>>>> [2] http://www.ecodataretriever.org/
>>>>>
>>>>>
>>>>> Matthew Collins
>>>>> Technical Operations Manager
>>>>> Advanced Computing and Information Systems Lab, ECE
>>>>> University of Florida
>>>>> 352-392-5414 <callto:352-392-5414>
>>>>> ------------------------------------------------------------------------
>>>>> *From:* jorrit poelen <jhpoelen at xs4all.nl>
>>>>> *Sent:* Monday, May 30, 2016 11:16 AM
>>>>> *To:* Collins, Matthew; Thompson, Alexander M; Hammock, Jennifer
>>>>> *Subject:* Fwd: [API-users] Is there any NEO4J or graph-based 
>>>>> driver for this API ?
>>>>> Hey y’all:
>>>>>
>>>>> Interesting request below on the GBIF mailing list - sounds like a 
>>>>> perfect fit for the GUODA use cases.
>>>>>
>>>>> Would it be too early to jump onto this thread and share our 
>>>>> efforts/vision?
>>>>>
>>>>> thx,
>>>>> -jorrit
>>>>>
>>>>>> Begin forwarded message:
>>>>>>
>>>>>> *From: *Jan Legind <jlegind at gbif.org>
>>>>>> *Subject: **Re: [API-users] Is there any NEO4J or graph-based 
>>>>>> driver for this API ?*
>>>>>> *Date: *May 30, 2016 at 5:48:51 AM PDT
>>>>>> *To: *Mauro Cavalcanti <maurobio at gmail.com>, "Juan M. Escamilla 
>>>>>> Molgora" <j.escamillamolgora at lancaster.ac.uk>
>>>>>> *Cc: *"api-users at lists.gbif.org 
>>>>>> <mailto:api-users at lists.gbif.org>" <api-users at lists.gbif.org>
>>>>>>
>>>>>> Dear Juan,
>>>>>> Unfortunately we have no tool for creating these kind of SQL like 
>>>>>> queries to the portal. I am sure you are aware that the filters 
>>>>>> in the occurrence search pages can be applied in combination in 
>>>>>> numerous ways. The API can go even further in this regard[1], but 
>>>>>> it not well suited for retrieving occurrence records since there 
>>>>>> is a 200.000 records ceiling making it unfit for species 
>>>>>> exceeding this number.
>>>>>> There is going be updates to the pygbif package[2] in the near 
>>>>>> future that will enable you to launch user downloads 
>>>>>> programmatically where a whole list of different species can be 
>>>>>> used as a query parameter as well as adding polygons.[3]
>>>>>> In the meantime, Mauro’s suggestion is excellent. If you can 
>>>>>> narrow your search down until it returns a manageable download 
>>>>>> (say less than 100 million records), importing this into a 
>>>>>> database should be doable. From there, you can refine using SQL 
>>>>>> queries.
>>>>>> Best,
>>>>>> Jan K. Legind, GBIF Data manager
>>>>>> [1]http://www.gbif.org/developer/occurrence#search
>>>>>> [2]https://github.com/sckott/pygbif
>>>>>> [3]https://github.com/jlegind/GBIF-downloads
>>>>>> *From:*API-users [mailto:api-users-bounces at lists.gbif.org]*On 
>>>>>> Behalf Of*Mauro Cavalcanti
>>>>>> *Sent:*30. maj 2016 14:06
>>>>>> *To:*Juan M. Escamilla Molgora
>>>>>> *Cc:*api-users at lists.gbif.org
>>>>>> *Subject:*Re: [API-users] Is there any NEO4J or graph-based 
>>>>>> driver for this API ?
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> One solution I have successfully adopted for this is to download 
>>>>>> the records (either "manually" via browser or, yet better, using 
>>>>>> a Python script using the fine pygbif library), storing them into 
>>>>>> a MySQL or SQLite database and then perform the relational 
>>>>>> queries. I can provide examples if you are interested.
>>>>>>
>>>>>> Best regards,
>>>>>> 2016-05-30 8:59 GMT-03:00 Juan M. Escamilla Molgora 
>>>>>> <j.escamillamolgora at lancaster.ac.uk>:
>>>>>> Hola,
>>>>>>
>>>>>> Is there any API for making relational queries like taxonomy, 
>>>>>> location or timestamp?
>>>>>>
>>>>>> Thank you and best wishes
>>>>>>
>>>>>> Juan
>>>>>> _______________________________________________
>>>>>> API-users mailing list
>>>>>> API-users at lists.gbif.org <mailto:API-users at lists.gbif.org>
>>>>>> http://lists.gbif.org/mailman/listinfo/api-users
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Dr. Mauro J. Cavalcanti
>>>>>> E-mail:maurobio at gmail.com
>>>>>> Web:http://sites.google.com/site/maurobio
>>>>>> _______________________________________________
>>>>>> API-users mailing list
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>>>>>> http://lists.gbif.org/mailman/listinfo/api-users
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>
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