Using CSV files is certainly simple and compact. And a one-level deep star structure around DwC makes a lot of sense to me. It is simple and simple works. ABCD, TCS are complex and suffer from the confining heirarchical, pyramid structures of XML in a world that is mainly relational. Star structures are the old stuff of data warehousing where efficiency and straightforward data updating is required.
But, isn't the age old problem with CSV files the weakness in integrity? One botched comma and you have a mess to troubleshoot. On a global scale, with thousands of providers, and hundreds of millions of records, any potential crack in the data integrity is potentially going to lead to a full-time job for someone to be tracking down the unexplainable errors. Working at these scales as Tim has pointed out forces consideration of small things that ordinarily are a breeze to contend with. Simple flat, tagged XML files (instead of CSV) in the same star structure could be a compromise. The files would be a little larger but have better integrity, and I would think they would compress well.
But, I like the general idea of using flat, one-level star structures.
Could we consider the same idea for harvesting name/concept data? A flat core with a one-level, one-to-many star. Rather than TCS.
Chuck
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Today's Topics:
1. Re: Fwd: Tapir protocol - Harvest methods? [SEC=UNCLASSIFIED] (Roger Hyam (TDWG)) 2. Re: [Hiscom-l] Fwd: Tapir protocol - Harvest methods? [SEC=UNCLASSIFIED] (Greg Whitbread)
----------------------------------------------------------------------
Message: 1 Date: Wed, 14 May 2008 10:57:20 +0100 From: "Roger Hyam (TDWG)" rogerhyam@mac.com Subject: Re: [tdwg-tapir] Fwd: Tapir protocol - Harvest methods? [SEC=UNCLASSIFIED] To: Markus D?ring mdoering@gbif.org Cc: "Hiscom-L Mailing List ((E-mail))" hiscom-l@chah.org.au, tdwg-tapir@lists.tdwg.org Message-ID: 16026031-3900-41BF-960D-17429360EFE6@mac.com Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes
Generally if we are going to have csv files for data transfer we don't need to have software implementations just some documentation on what the csv files should contain. Something along the lines of:
1) Make a report from your database as a csv file(s) with the following columns... 2) Zip it up. 3) Either put it on a webserver and send us the URL or upload it using this webform.
We don't need to bother with TAPIR etc. You could even only produce a CSV file of the records that have changed so big data sets needn't be a problem.
I worry that we are working out how to move data about quickly and forgetting that the real goal is to integrate data and that will only come if people have GUIDs on the stuff they own and use other peoples GUIDs in their data. Solutions based around CSV files do nothing to move people in that direction and I would suspect lead to making matters worse.
Finding ourselves in hole digging quicker may not be the best option.
Roger
------------------------------------------------------------- Roger Hyam Roger@BiodiversityCollectionsIndex.org http://www.BiodiversityCollectionsIndex.org ------------------------------------------------------------- Royal Botanic Garden Edinburgh 20A Inverleith Row, Edinburgh, EH3 5LR, UK Tel: +44 131 552 7171 ext 3015 Fax: +44 131 248 2901 http://www.rbge.org.uk/ -------------------------------------------------------------
On 14 May 2008, at 10:21, Markus D?ring wrote:
Interesting that we all come to the same conclusions... The trouble I had with just a simple flat csv file is repeating properties like multiple image urls. ABCD clients dont use ABCD just because its complex, but because they want to transport this relational data. We were considering 2 solutions to extending this csv approach. The first would be to have a single large denormalised csv file with many rows for the same record. It would require knowledge about the related entities though and could grow in size rapidly. The second idea which we think to adopt is allowing a single level of 1- many related entities. It is basically a "star" design with the core dwc table in the center and any number of extension tables around it. Each "table" aka csv file will have the record id as the first column, so the files can be related easily and it only needs a single identifier per record and not for the extension entities. This would give a lot of flexibility while keeping things pretty simple to deal with. It would even satisfy the ABCD needs as I havent yet seen anyone requiring 2 levels of related tables (other than lookup tables). Those extensions could even be a simple 1-1 relation, but would keep things semantically together just like a xml namespace. The darwin core extensions would be good for example.
So we could have a gzipped set of files, maybe with a simple metafile indicating the semantics of the columns for each file. An example could look like this:
# darwincore.csv 102 Aster alpinus subsp. parviceps ... 103 Polygala vulgaris ...
# curatorial.csv 102 Kew Herbarium 103 Reading Herbarium
# identification.csv 102 2003-05-04 Karl Marx Aster alpinus L. 102 2007-01-11 Mark Twain Aster korshinskyi Tamamsch. 102 2007-09-13 Roger Hyam Aster alpinus subsp. parviceps Novopokr. 103 2001-02-21 Steve Bekow Polygala vulgaris L.
I know this looks old fashioned, but it is just so simple and gives us so much flexibility. Markus
On 14 May, 2008, at 24:39, Greg Whitbread wrote:
We have used a very similar protocol to assemble the latest AVH cache. It should be noted that this is an as-well-as protocol that only works because we have an established semantic standard (hispid/abcd).
greg
trobertson@gbif.org wrote:
Hi All,
This is very interesting too me, as I came up with the same conclusion while harvesting for GBIF.
As a "harvester of all records" it is best described with an example:
- Complete Inventory of ScientificNames: 7 minutes @ the limited 200
records per page
- Complete Harvesting of records:
- 260,000 records
- 9 hours harvesting duration
- 500MB TAPIR+DwC XML returned (DwC 1.4 with geospatial and
curatorial extensions)
- Extraction of DwC records from harvested XML: <2 minutes
- Resulting file size 32MB, Gzipped to <3MB
I spun hard drives for 9 hours, and took up bandwidth that is paid for, to retrieve something that could have been generated provider side in minutes and transferred in seconds (3MB).
I sent a proposal to TDWG last year termed "datamaps" which was effectively what you are describing, and I based it on the Sitemaps protocol, but I got nowhere with it. With Markus, we are making more progress and I have spoken with several GBIF data providers about a proposed new standard for full dataset harvesting and it has been received well. So Markus and I have started a new proposal and have a working name of 'Localised DwC Index' file generation (it is an index if you have more than DwC data, and DwC is still standards compliant) which is really a GZipped Tab file dump of the data, which is slightly extensible. The document is not ready to circulate yet but the benefits section reads currently:
- Provider database load reduced, allowing it to serve real
distributed queries rather than "full datasource" harvesters
- Providers can choose to publish their index as it suits them,
giving control back to the provider
- Localised index generation can be built into tools not yet
capable of integrating with TDWG protocol networks such as GBIF
- Harvesters receive a full dataset view in one request, making it
very easy to determine what records are eligible for deletion
- It becomes very simple to write clients that consume entire
datasets. E.g. data cleansing tools that the provider can run:
- Give me ISO Country Codes for my dataset
- The application pulls down the providers index file,
generates ISO country code, returns a simple table using the providers own identifier
- Check my names for spelling mistakes
- Application skims over the records and provides a list that
are not known to the application
- Providers such as UK NBN cannot serve 20 million records to the
GBIF index using the existing protocols efficiently.
- They have the ability to generate a localised index however
- Harvesters can very quickly build up searchable indexes and it is
easy to create large indices.
- Node Portal can easily aggregate index data files
- true index to data, not an illusion of a cache. More like Google
sitemaps
It is the ease at which one can offer tools to data providers that really interests me. The technical threshold required to produce services that offer reporting tools on peoples data is really very low with this mechanism. This and the fact that large datasets will be harvestable - we have even considered the likes of bit-torrent for the large ones although I think this is overkill.
As a consumer therefore I fully support this move as a valuable addition to the wrapper tools.
Cheers
Tim (wrote the GBIF harvesting, and new to this list)
Begin forwarded message:
From: "Aaron D. Steele" eightysteele@gmail.com Date: 13 de mayo de 2008 22:40:09 GMT+02:00 To: tdwg-tapir@lists.tdwg.org Cc: Aaron Steele asteele@berkeley.edu Subject: Re: [tdwg-tapir] Tapir protocol - Harvest methods?
at berkeley we've recently prototyped a simple php program that uses an existing tapirlink installation to periodically dump tapir resources into a csv file. the solution is totally generic and can dump darwin core (and technically abcd schema, although it's currently untested). the resulting csv files are zip archived and made accessible using a web service. it's a simple approach that has proven to be, at least internally, quite reliable and useful.
for example, several of our caching applications use the web service to harvest csv data from tapirlink resources using the following process:
- download latest csv dump for a resource using the web service.
- flush all locally cached records for the resource.
- bulk load the latest csv data into the cache.
in this way, cached data are always synchronized with the resource and there's no need to track new, deleted, or changed records. as an aside, each time these cached data are queried by the caching application or selected in the user interface, log-only search requests are sent back to the resource.
after discussion with renato giovanni and john wieczorek, we've decided that merging this functionality into the tapirlink codebase would benefit the broader community. csv generation support would be declared through capabilities. although incremental harvesting wouldn't be immediately implemented, we could certainly extend the service to include it later.
i'd like to pause here to gauge the consensus, thoughts, concerns, and ideas of others. anyone?
thanks, aaron
2008/5/5 Kevin Richards RichardsK@landcareresearch.co.nz:
I think I agree here.
The harvesting "procedure" is really defined outside the Tapir protocol, is it not? So it is really an agreement between the harvester and the harvestees.
So what is really needed here is the standard procedure for maintaining a "harvestable" dataset and the standard procedure for harvesting that dataset. We have a general rule at Landcare, that we never delete records in our datasets - they are either deprecated in favour of another record, and so the resolution of that record would point to the new record, or the are set to a state of "deleted", but are still kept in the dataset, and can be resolved (which would indicate a state of deleted).
Kevin
>>> "Renato De Giovanni" renato@cria.org.br 6/05/2008 7:33 a.m. >>>>>>
Hi Markus,
I would suggest creating new concepts for incremental harvesting, either in the data standards themselves or in some new extension. In the case of TAPIR, GBIF could easily check the mapped concepts before deciding between incremental or full harvesting.
Actually it could be just one new concept such as "recordStatus" or "deletionFlag". Or perhaps you could also want to create your own definition for dateLastModified indicating which set of concepts should be considered to see if something has changed or not, but I guess this level of granularity would be difficult to be supported.
Regards,
Renato
On 5 May 2008 at 11:24, Markus D?ring wrote:
> Phil, > incremental harvesting is not implemented on the GBIF side as > far > as I > am aware. And I dont think that will be a simple thing to > implement on > the current system. Also, even if we can detect only the changed > records since the last harevesting via dateLastModified we still > have > no information about deletions. We could have an arrangement > saying > that you keep deleted records as empty records with just the ID > and > nothing else (I vaguely remember LSIDs were supposed to work > like > this > too). But that also needs to be supported on your side then, > never > entirely removing any record. I will have a discussion with the > others > at GBIF about that. > > Markus _______________________________________________ tdwg-tapir mailing list tdwg-tapir@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir
Please consider the environment before printing this email
WARNING : This email and any attachments may be confidential and/ or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments.
The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. http:// www.landcareresearch.co.nz _______________________________________________ tdwg-tapir mailing list tdwg-tapir@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir
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Australian Centre for Plant BIodiversity Research<------------------+ National greg whitBread voice: +61 2 62509 482 Botanic Integrated Botanical Information System fax: +61 2 62509 599 Gardens S........ I.T. happens.. ghw@anbg.gov.au +----------------------------------------->GPO Box 1777 Canberra 2601
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments.
Please consider the environment before printing this email.
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------------------------------
Message: 2 Date: Wed, 14 May 2008 19:59:12 +1000 From: "Greg Whitbread" ghw@anbg.gov.au Subject: Re: [tdwg-tapir] [Hiscom-l] Fwd: Tapir protocol - Harvest methods? [SEC=UNCLASSIFIED] To: "Markus D?ring " mdoering@gbif.org Cc: "Hiscom-L Mailing List ((E-mail))" hiscom-l@chah.org.au, tdwg-tapir@lists.tdwg.org Message-ID: 1210759152.18436.414.camel@goshawk Content-Type: text/plain; charset=utf-8
Marcus,
We have used the star technique with abcd with some success. The core is pretty close to dwc if the current determination goes there too. It can then be delivered with headers appropriate to the harvester's preference. It gets harder when we try to do tcs.
On Wed, 2008-05-14 at 19:21, Markus D?ring wrote:
Interesting that we all come to the same conclusions... The trouble I had with just a simple flat csv file is repeating properties like multiple image urls. ABCD clients dont use ABCD just because its complex, but because they want to transport this relational data. We were considering 2 solutions to extending this csv
approach. The first would be to have a single large denormalised csv file with many rows for the same record. It would require knowledge about the related entities though and could grow in size rapidly. The
second idea which we think to adopt is allowing a single level of 1- many related entities. It is basically a "star" design with the core dwc table in the center and any number of extension tables around it.
Each "table" aka csv file will have the record id as the first column,
so the files can be related easily and it only needs a single identifier per record and not for the extension entities. This would give a lot of flexibility while keeping things pretty simple to deal with. It would even satisfy the ABCD needs as I havent yet seen anyone
requiring 2 levels of related tables (other than lookup tables). Those
extensions could even be a simple 1-1 relation, but would keep things
semantically together just like a xml namespace. The darwin core extensions would be good for example.
So we could have a gzipped set of files, maybe with a simple metafile
indicating the semantics of the columns for each file. An example could look like this:
# darwincore.csv 102 Aster alpinus subsp. parviceps ... 103 Polygala vulgaris ...
# curatorial.csv 102 Kew Herbarium 103 Reading Herbarium
# identification.csv 102 2003-05-04 Karl Marx Aster alpinus L. 102 2007-01-11 Mark Twain Aster korshinskyi Tamamsch. 102 2007-09-13 Roger Hyam Aster alpinus subsp. parviceps Novopokr. 103 2001-02-21 Steve Bekow Polygala vulgaris L.
I know this looks old fashioned, but it is just so simple and gives us
so much flexibility. Markus
On 14 May, 2008, at 24:39, Greg Whitbread wrote:
We have used a very similar protocol to assemble the latest AVH
cache.
It should be noted that this is an as-well-as protocol that only
works
because we have an established semantic standard (hispid/abcd).
greg
trobertson@gbif.org wrote:
Hi All,
This is very interesting too me, as I came up with the same conclusion while harvesting for GBIF.
As a "harvester of all records" it is best described with an
example:
- Complete Inventory of ScientificNames: 7 minutes @ the limited
200
records per page
- Complete Harvesting of records:
- 260,000 records
- 9 hours harvesting duration
- 500MB TAPIR+DwC XML returned (DwC 1.4 with geospatial and
curatorial extensions)
- Extraction of DwC records from harvested XML: <2 minutes
- Resulting file size 32MB, Gzipped to <3MB
I spun hard drives for 9 hours, and took up bandwidth that is paid
for, to retrieve something that could have been generated provider side in
minutes and transferred in seconds (3MB).
I sent a proposal to TDWG last year termed "datamaps" which was effectively what you are describing, and I based it on the Sitemaps protocol, but I got nowhere with it. With Markus, we are making
more
progress and I have spoken with several GBIF data providers about a proposed new standard for full dataset harvesting and it has been received well. So Markus and I have started a new proposal and have a working name of 'Localised DwC Index' file generation (it is an index if you have more than DwC data, and DwC is still standards compliant) which is really a GZipped Tab file dump of the data, which is slightly extensible.
The
document is not ready to circulate yet but the benefits section
reads
currently:
- Provider database load reduced, allowing it to serve real
distributed queries rather than "full datasource" harvesters
- Providers can choose to publish their index as it suits them,
giving control back to the provider
- Localised index generation can be built into tools not yet
capable of integrating with TDWG protocol networks such as GBIF
- Harvesters receive a full dataset view in one request, making it
very easy to determine what records are eligible for deletion
- It becomes very simple to write clients that consume entire
datasets. E.g. data cleansing tools that the provider can run:
- Give me ISO Country Codes for my dataset
- The application pulls down the providers index file,
generates ISO country code, returns a simple table using the providers own identifier
- Check my names for spelling mistakes
- Application skims over the records and provides a list that
are not known to the application
- Providers such as UK NBN cannot serve 20 million records to the
GBIF index using the existing protocols efficiently.
- They have the ability to generate a localised index however
- Harvesters can very quickly build up searchable indexes and it is
easy to create large indices.
- Node Portal can easily aggregate index data files
- true index to data, not an illusion of a cache. More like Google
sitemaps
It is the ease at which one can offer tools to data providers that
really interests me. The technical threshold required to produce services
that offer reporting tools on peoples data is really very low with this mechanism. This and the fact that large datasets will be harvestable - we have even considered the likes of bit-torrent for the large ones although I think this is overkill.
As a consumer therefore I fully support this move as a valuable addition to the wrapper tools.
Cheers
Tim (wrote the GBIF harvesting, and new to this list)
Begin forwarded message:
From: "Aaron D. Steele" eightysteele@gmail.com Date: 13 de mayo de 2008 22:40:09 GMT+02:00 To: tdwg-tapir@lists.tdwg.org Cc: Aaron Steele asteele@berkeley.edu Subject: Re: [tdwg-tapir] Tapir protocol - Harvest methods?
at berkeley we've recently prototyped a simple php program that uses an existing tapirlink installation to periodically dump tapir resources into a csv file. the solution is totally generic and
can
dump darwin core (and technically abcd schema, although it's currently untested). the resulting csv files are zip archived and made accessible using a web service. it's a simple approach that has proven to be, at least internally, quite reliable and useful.
for example, several of our caching applications use the web service to harvest csv data from tapirlink resources using the following process:
- download latest csv dump for a resource using the web service.
- flush all locally cached records for the resource.
- bulk load the latest csv data into the cache.
in this way, cached data are always synchronized with the resource and there's no need to track new, deleted, or changed records. as an aside, each time these cached data are queried by the caching application or selected in the user interface, log-only search requests are sent back to the resource.
after discussion with renato giovanni and john wieczorek, we've decided that merging this functionality into the tapirlink
codebase
would benefit the broader community. csv generation support would
be declared through capabilities. although incremental harvesting wouldn't be immediately implemented, we could certainly extend
the
service to include it later.
i'd like to pause here to gauge the consensus, thoughts, concerns, and ideas of others. anyone?
thanks, aaron
2008/5/5 Kevin Richards RichardsK@landcareresearch.co.nz:
I think I agree here.
The harvesting "procedure" is really defined outside the Tapir protocol, is it not? So it is really an agreement between the harvester and
the harvestees.
So what is really needed here is the standard procedure for maintaining a "harvestable" dataset and the standard procedure for harvesting
that dataset. We have a general rule at Landcare, that we never delete records
in our datasets - they are either deprecated in favour of another
record,
and so the resolution of that record would point to the new record, or
the are set to a state of "deleted", but are still kept in the dataset, and
can be resolved (which would indicate a state of deleted).
Kevin
>>> "Renato De Giovanni" renato@cria.org.br 6/05/2008 7:33 a.m.
>>> >>>
Hi Markus,
I would suggest creating new concepts for incremental
harvesting,
either in the data standards themselves or in some new extension. In the case of TAPIR, GBIF could easily check the mapped concepts before deciding between incremental or full harvesting.
Actually it could be just one new concept such as "recordStatus"
or "deletionFlag". Or perhaps you could also want to create your
own
definition for dateLastModified indicating which set of concepts should be considered to see if something has changed or not, but
I
guess this level of granularity would be difficult to be supported.
Regards,
Renato
On 5 May 2008 at 11:24, Markus D?ring wrote:
> Phil, > incremental harvesting is not implemented on the GBIF side as
far
> as I > am aware. And I dont think that will be a simple thing to > implement on > the current system. Also, even if we can detect only the
changed
> records since the last harevesting via dateLastModified we
still
> have > no information about deletions. We could have an arrangement > saying > that you keep deleted records as empty records with just the ID
> and > nothing else (I vaguely remember LSIDs were supposed to work
like
> this > too). But that also needs to be supported on your side then, > never > entirely removing any record. I will have a discussion with the > others > at GBIF about that. > > Markus _______________________________________________ tdwg-tapir mailing list tdwg-tapir@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir
Please consider the environment before printing this email
WARNING : This email and any attachments may be confidential
and/
or privileged. They are intended for the addressee only and are not
to be read, used, copied or disseminated by anyone receiving them in error.
If
you are not the intended recipient, please notify the sender by return email and delete this message and any attachments.
The views expressed in this email are those of the sender and do
not necessarily reflect the official views of Landcare Research. http:// www.landcareresearch.co.nz _______________________________________________ tdwg-tapir mailing list tdwg-tapir@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir
tdwg-tapir mailing list tdwg-tapir@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir
tdwg-tapir mailing list tdwg-tapir@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir
--
Australian Centre for Plant BIodiversity
Research<------------------+
National greg whitBread voice: +61 2 62509
482
Botanic Integrated Botanical Information System fax: +61 2 62509
599
Gardens S........ I.T. happens..
ghw@anbg.gov.au
+----------------------------------------->GPO Box 1777 Canberra
2601
If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright
in respect of information in the e-mail or attachments.
Please consider the environment before printing this email.
tdwg-tapir mailing list tdwg-tapir@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir
Hiscom-l mailing list Hiscom-l@chah.org.au http://chah.org.au/mailman/listinfo/hiscom-l_chah.org.au