Tuesday, 8 May 2007

Tapir, LSIDs and TDWG and what it all means...

More on the categorising of flora and fauna. Following on from my post of 1st May, here, a discussion with Paul and Lynda has clarified a bit more about what all the acronyms mean and what the plans for the future are.

LSIDs are a categorising system that sets out to bring digital collections management in biodiversity up to a web 2.0 standard. Ideally it replaces and encompasses the two previous standards for flora and fauna, makes the data accessible and searchable, and allows much greater aggregation of data.
In a practical sense, what this means is that you can search for and find an object (which can be an actual specimen, but not only a specimen!), and then, using its LSID, locate other objects related to it by location, by species, by characteristics, by institution, or by any information that is conveyed by the LSID.

To borrow from the LSID website:

Every LSID consists of up to five parts: the Network Identifier (NID); the root DNS name of the issuing authority; the namespace chosen by the issuing authority; the object id unique in that namespace; and finally an optional revision id for storing versioning information. Each part is separated by a colon to make LSIDs easy to parse.


So what does this do for the biodiversity community? Well, if museums et al take up the system, it means that all this data is available online: for research purposes, for species monitoring, for mapping and locating endangered and rare species, and so enabling a greater and more immediate response to management and planning for the future. Again, the Hennes article comes to mind, with its discussion about the future possibilities for museums and their collections.



How is it implemented?
Unlike other online cataloguing systems, this would be applied at the level of the institution. If the institution already has a DOI system in place, it may need tweaking to comply with LSID standards. The internal museum system would not have to be changed, however, as the LSID is divided into component parts (described above).
It is overseen by TAPIR (TDWG Access Protocol for Information Retrieval)
As the website says:



TAPIR combines and extends features of the BioCASe and DiGIR protocols to create a new and more generic means of communication between client applications and data providers using the Internet.


So, TAPIR oversees the implementation of the protocol. If you feel brave enough to tackle a sea of acronyms you can check out the TAPIR wiki.

Please let me know if any of this is inaccurate, i have done my best to put it in layperson terms. Conceptually it sounds like a great idea to me. We also discussed The machine is eating us, as an example of a great way to convey what are conceptually complicated ideas in a simple, effective, interesting format. Are there other, successful ways to deal with these issues in a very short timeframe? that is the upcoming challenge.

23 comments:

LyndaK said...

Several weeks ago Jesse Ausubel, Chair of the Board of the "http://www.eol.org/">Encyclopedia of Life gave a talk at the Museum. They have recently launched their website and the FAQ page gives a good overview of this ambitious project.

Basically the premise is to have "a web site for every species" which contains, not only general information about a species, but an underlying archivce of all scientific papers and other related material as part of the species record.

As Jesse said in his presentation:
“Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. The page contains the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits. The page opens out directly or by linking to other databases ... It comprises a summary of everything known about the species’ genome, proteome, geographical distribution, phylogenetic position, habitat, ecological relationships and, not least, its perceived practical importance for humanity."

This sounds like something to keep on top of, and I'm wondering if the LSID/TDWG group will be involved somehow??

LyndaK said...

Mel: Lee Belbin, Manager of the TDWG Infrastructure Project mentioned that they would like two stories/videos about the LSID/TDWG projects. The examples he gave us that they like are The Machine is Us/ing Us and The Encyclopedia of Life - the EOL I haven't seen before and it's totally cool (but looks expensive...).

At this stage I think we should run a thread on the TDWG blog and invite both generalists and specialists into our conversation. What do others think?

leebel said...

TDWG is indeed involved with the EoL project. In fact TAPIR + LSIDs are two key components of GBIF's Universal Biodiversity Data Bus (UBDB or as Paddy from EoL calls it - the Oobe Doobie). EoL has stated that it would use TDWG standards when it came to moving 'biodiversity' data around - which is a BIG part of what EoL will do. LSIDs will become the the core identifiers of biological (or any other type) of object, and TAPIR provides the mechanism to query and aggregate responses across the network.

mel said...

I don't think it really matters where it is, especially if we are interested in testing the use of blogging in the first place, and how it works (or doesn't) for the museum. having said that, i am happy to converse anywhere, as long as there is someone who can explain the acronysms to me!
We are certainly off to a good start already.

leebel said...

The TDWG Blog is being setup in the next hour or so to accept posts from any user registered on the TDWG site (see http://www.tdwg.org/membership/registration/).

The blog has an RSS feed at http://www.tdwg.org/blog/rss.xml.

Also of interest: The EoL project just hit Newsweek (http://www.msnbc.msn.com/id/18580428/site/newsweek/) with a prominant mention of the 'inspirational video'.

Things are really hotting up in the biodiversity arena! A good thing.

LyndaK said...

Thanks Lee - I've signed up and am looking forward to working in the wonderful world of acronyms!

Renato said...

Mel, regarding TAPIR and the idea of making a video, you probably don't need to worry about most acronyms and strange names that you find in the Wiki. Sometimes they are related to historical things, like the previous protocols DiGIR and BioCASe; sometimes they are related to the software implementations, like PyWrapper and TapirLink; sometimes they are related to other data standards that can be exchanged through TAPIR, like ABCD, DarwinCore, TCS; sometimes they are related to similar technologies, like WFS.

In my opinion none of these things are worth mentioning in a video for a non-technical audience. The most important thing is to grasp the main idea of TAPIR, understand how it works and what it can do. A good starting point is the executive summary that we just prepared (it's only a first version, so we're welcoming any suggestions).

By the way, I somehow always associate TAPIR with the idea of "unleashing data". It also comes to my mind a picture of someone opening a drawer full of specimens. TAPIR allows many database drawers to open at the same time to deliver you the data you want...

mel said...

Renato
that's a very good executive summary - it makes TAPIR much clearer. I also like the analogy of the drawers, filled with specimens, being opened - a nice visual metaphor.
In technical terms, is it anything like using php and My SQL to mine a database?
I am glad you defined the audience, it makes the project simpler. Lynda mentioned two stories - is one about LSIDs and one about TAPIR?

Renato said...

Yes, I think Lee mentioned two videos: one for TAPIR and another for LSIDs.

About your comparison with PHP and MySQL, I'm not sure what kind of similarities you're trying to find.

- PHP and a MySQL database: There's only one database with a specific data structure. You write a PHP script that conects to the database and then you send one or more SQL queries to get the data you want.

- TAPIR network: There are several addresses on the Web (TAPIR accesspoints) that can be used to communicate with TAPIR data providers. You can use some kind of yellow pages service to discover these addresses. Once you have them, you can write a script in your favourite language to interact with the services. It's good practice to make sure that all services use the same abstraction layer and have the necessary capabilities before sending search requests. If these conditions are met, your script can interact in parallel with all services. A search request to one specific service can look like:

http://example.net/col_x?op=search&
m=*&filter=genus equals "Thylacinus"

* = address to an output model indicating the format of the response.

In this example, genus would actually be something like http://rs.tdwg.org/dwc/dwcore/Genus which is an identifier of a concept from DarwinCore. For each TAPIR provider using DarwinCore, this concept will be "mapped" to a specific field in a database.

This way you can remotely interact with many data providers without worrying about their operating system, type of database and database structure.

Trying to explain in a different way, if you want to use PHP for the task, instead of connecting to a MySQL database and sendng SQL queries, you will need to connect to several internet addresses sending HTTP requests according to the TAPIR protocol and then parsing the XML responses.

Not sure if this helps your understanding or not...

mel said...

Thanks Renato, I had another look at the executive summary and I think the mist is clearing...I think it is good to have this exchange, especially considering the videos will be aimed at the scientific layperson, which is what I am! And like anyone, to understand the concepts I look for analogies to areas I already know.

I keep returning to your metaphor of the opening drawers, and perhaps the next step from here would be an example of what data/info TAPIR (and LSID) allows you to see, compared to previous methods of data access.

FluaP said...

I have set up a blog on the TDWG site now - you can get there thru
:-
http://www.tdwg.org/blog/blog-article/article/digital-stories-for-tapir-and-lsid/

You will need to register to comment

FluaP said...

I have posted at TDWG - please go there to contribute
http://www.tdwg.org/blog/blog-article/article/digital-stories-for-tapir-and-lsid/

mel said...

This discussion is continuing over at TDWIG blog, with a dialogue on digital story development to explain TAPIR and LSID underway. please check this out

car-finance-team said...

Car Finance Team think this is interesting discussion for special person.

I've added knowledge more by read this discussion.

thanks.

http://www.usome.com said...

有什么 有什么网址 有什么新闻 有什么博客 有什么论文 有什么爱秀
有什么图片 有什么音乐 有什么搜商 有什么帖客 天气预报

烟雨遥 said...

你认为好的优化技术不要总跟在别人后面
网络营销永远不可能超越对手
易网必得|网站地图
SEOSEO文章
最近这几天比较忙,也很少有时间顾的上去写SEO文章了。毕竟自身是一个比较懒散的人。Zac坚持seo优化排名每天一贴,跟这样的老前辈比起来,


怎样进行对一个网站的seo优化分析呢?

seo技术总结起来就是一个字“细”,SEM博客地图总结:我们在做seo时不要去拘泥与现状
网站优化,要总结分析最新最好的技术、
seo技术在总结时也要自己去创新。
易网必得只有这样去做seo优化才是成功的优化,让对手永远摸不着你,让对手停留在你的后面去追赶你。SEO培训北京SEOgoogle左侧排名做seo其实很简单,就是考验一个人耐心、恒心、信心、分析能力。相信自己比对手做的更好。你就会得到发展北京seo

节能、环保节能锅炉锅炉、
易网必得提供相关文章

google优化 said...

无锡乐洋化机公司主要采购反应设备销售反应设备反应设备商机反应设备产品反应设备公司反应设备供应商反应设备市场反应设备价格行情
反应设备展会信息反应设备行业资讯反应设备
反应设备

本公司主要生产反应设备销售反应设备制造反应设备和各种产品我们是反应设备供应商有很大的反应设备市场反应设备详细情况可以访问反应设备专业网站

fanzhijie said...

wow gold
wow gold
wow power leveling
wow power leveling
wow gold@@@@
World of Warcraft Gold
wow power leveling
wow power leveling
wow power leveling
wow power leveling
wow power leveling
wow power leveling
wow power leveling
wow power leveling
wow power leveling
wow powerleveling
wow powerleveling
wow powerleveling
rolex replica
wow powerleveling
wow powerleveling
wow powerleveling
wow powerleveling
wow powerleveling
wow powerleveling
wow powerleveling
wow powerleveling
replica rolex
powerleveling
powerleveling
powerleveling
powerleveling
power leveling
power leveling
powerleveling
powerleveling
power leveling
power leveling
power leveling
power leveling
power leveling
power leveling
power leveling
power leveling
rolex
wow gold
wow gold
Warcraft Gold
Warcraft Gold

中高年 転職
アルバイト 求人情報
ブライダル
転職
競馬
FX
ダイエット
お見合い
競馬 予想
新築マンション
新築マンション
コンタクトレンズ
婚約指輪
合宿免許
人材派遣
東京都 墓地
派遣会社
人材派遣
パチンコ 攻略
おなら

货架
OCR
OCR
手机词典
高速扫描
机票
灭蟑螂
蜗轮减速机
减速机
齿轮减速机
丝杆升降机
租房
租房
北京租房
北京租房
搬家公司
北京搬家
北京搬家公司
上海机票
上海机票
上海打折机票
上海打折机票
上海特价机票
上海特价机票
搬家公司
搬家公司
北京搬家公司
北京搬家公司

vcbcvbvnfghf

tonyparker said...

wow gold
cheap wow gold
buy wow gold
world of warcraft gold
wow
world of warcraft
wow gold
WoW Warrior
WoW Hunter
WoW Rogue
WoW Paladin
WoW Shaman
WoW Priest
WoW Mage
WoW Druid
WoW Warlock
google排名
google左侧排名
google排名服务
百度推广
百度排名
机床
LED灯
电池
塑料
摄像机
电动车
包装设计
移民
甲醇
染料
体育博客
股票博客
游戏博客
魔兽博客
考试博客
logo design
website design
web design
商标设计

titi said...

runescape money runescape gold runescape gold buy runescape gold runescape money runescape gold wow power leveling wow powerleveling Warcraft Power Leveling Warcraft PowerLeveling buy runescape gold buy runescape money runescape itemsrunescape accounts runescape gp dofus kamas buy dofus kamas Guild Wars Gold buy Guild Wars Gold lotro gold buy lotro gold lotro gold buy lotro gold lotro gold buy lotro gold runescape money runescape power leveling runescape money runescape gold dofus kamas cheap runescape money cheap runescape gold Hellgate Palladium Hellgate London Palladium Hellgate money Tabula Rasa gold tabula rasa money Tabula Rasa Credit Tabula Rasa Credits Hellgate gold Hellgate London gold wow power leveling wow powerleveling Warcraft PowerLeveling Warcraft Power Leveling World of Warcraft PowerLeveling World of Warcraft Power Leveling runescape power leveling runescape powerleveling eve isk eve online isk eve isk eve online isk tibia gold Fiesta Silver Fiesta Gold SilkRoad Gold buy SilkRoad Gold runescape accounts buy runescape accounts rs2 accounts buy rs2 accounts runescape power leveling rs2 power leveling FFXI Gil buy FFXI Gil buy dofus kamas buy dofus kamas dofus kamas
runescape accounts
buy runescape accounts
rs2 accounts
buy rs2 accounts
runescape power leveling
rs2 power leveling

qweaq said...

1.
Welcome to enter (wow gold) and (wow power leveling) trading site, (Rolex) are cheap, (World of Warcraft gold) credibility Very good! Quickly into the next single! Key words directly to the website click on transactions!

2.
Welcome to enter (wow gold) and (wow power leveling) trading site, (wow gold) are cheap, (wow power leveling) credibility Very good! Quickly into the next single! Key words directly to the website click on transactions!

3.
Welcome to enter (wow gold) and (wow power leveling) trading site, (wow gold) are cheap, (wow power leveling) credibility Very good! Quickly into the next single! Key words directly to the website click on transactions!

北京现代 said...

shanghai hotel
guangzhou hotel
shenzhen hotel
beijing hotel
guangzhou hotel
Shenzhen hotel
shanghai hotel
beijing hotel
回转支承
转盘轴承
slewing ring
slewing bearing
slewing bearings
china hotel

www.shoesorder.biz said...

http://www.shoesorder.biz
http://www.shoesshop.biz
http://www.nikexshoes.com

we can provide most of style,we are wholesale, we sell style shoes as follows: Nike Air Max 87 88 90 95 97 180 360 2003 2007 Ltd Plus Tn 8. Nike Shox NZ OZ VC De R2 R3 R4 R5 Zoom TL 3 Rival Torch Flight Bmw Turbo Monster CL Classic Shoes Testify Leaper. Nike Air Force 1 25 XXV One Low I High Clear Shoes Light Bird's Nest Supreme. Nike Free 7.0 5.0 4.0 3.0.Nike Air Dunk Low SB Mid High Rift Air Stab 89 Foamposite Kobe Basketball Shoes. Nike Air Jordan Retro 1-23 + AF1 Spizike Dub Zero. Nike Lebron James 2 3 4 5 Low Zoom Soldier. Dolce Gabbana Bape Star Sta DG Ice Cream Gucci Lacoste Shoes Leather Prada UGG Timberland boots. Converse All Star One Wade 1 2 3 Puma Ferrari Running Shoes Osu Fluxion Bmw Sauber F1 Team. Adidas Shoes T-Mac Samba Gazelle Garnett Adicolor Adiprene Country Gil Zero Dragon NBA Goodyear Stan Smith Beijing 2008 Superstar 35 Climacool Football Shoes City Series.

Contact Us:
msn message: Shoesorder@msn.com
Email: Shoesorder@yeah.net

Nike Air Max 87
Nike Air Max 88
Nike Air Max 90
Nike Air Max 95
Nike Air Max 97
Nike Air Max 180
Nike Air Max 360
Nike Air Max Ltd
Nike Air Max 2003
Nike Air Max 2007
Nike Air Max Tn
Nike Air Max Plus Tn 8
Nike Shox NZ
Nike Shox OZ
Nike Shox VC
Nike Shox R2
Nike Shox R3
Nike Shox R4
Nike Shox R5
Nike Shox TL
Nike Shox TL 3
Nike Shox Bmw
Nike Shox Zoom
Nike Shox Rival
Nike Shox Torch
Nike Shox Turbo
Nike Shox Leaper
Nike Shox Flight
Nike Shox Testify
Nike Shox Monster
Nike Shox Classic
Nike Air Jordan 1
Nike Air Jordan 2
Nike Air Jordan 3
Nike Air Jordan 4
Nike Air Jordan 5
Nike Air Jordan 6
Nike Air Jordan 7
Nike Air Jordan 8
Nike Air Jordan 9
Nike Air Jordan 10
Nike Air Jordan 11
Nike Air Jordan 12
Nike Air Jordan 13
Nike Air Jordan 14
Nike Air Jordan 17
Nike Air Jordan 19
Nike Air Jordan 20
Nike Air Jordan 21
Nike Air Jordan 22
Nike Air Jordan 23
Nike Jordan 7.5
Nike Jordan Spizike
Nike Jordan 7 Clear
Nike Jordan Dub Zero
Air Jordan 3 + AF1
Air Jordan 5 + AF1
Air Jordan 12 + AF1
Air Jordan 23 + AF1
Nike Air Dunk
Nike Dunk High
Nike Free 3.0
Nike Free 4.0
Nike Free 5.0
Nike Free 7.0
Nike Lebron James
Nike James Lebron 3
Nike James Lebron 4
Nike Lebron James 5
Nike Lebron Soldier
Nike Zoom Lebron Low
Nike Air Force 1
Nike Air Force 25
Nike Air Force One
Nike Air Force 1 High
Nike Air Force 1 Light
Nike Air Force 1 Clear
Nike Air Force 1 Supreme
Nike Air Force 1 Bird's Nest
Nike Air Rift
Nike Air Stab 89
Nike Air Foamposite
Nike Bird's Nest
Nike Football Shoes
Nike Zoom Kobe
Nike Zoom
Nike Shoes
Bape Sta
Bape Star
Bape Sta Air
Bape Sta High
Bape Star Logo
Bape Star Clear
Adidas Shoes
Adidas T-Mac
Adidas Samba
Adidas Dragon
Adidas Gazelle
Adidas Garnett
Adidas Country
Adidas adiPRENE
Adidas Gil Zero
Adidas Adicolor
Adidas NBA Shoes
Adidas Good Year
Adidas Climacool
Adidas Stan Smith
Adidas Bird's Nest
Adidas City Series
Adidas Superstar 35Th
Adidas Beijing 2008
Adidas Football shoes
Puma Shoes
Puma Osu Shoes
Puma Ferrari Shoes
Puma Fluxion Shoes
Puma Running Shoes
Puma Bmw Sauber F1 Team
Converse Shoes
Converse All Star
Converse One Star
Converse High
Converse Wade 1 2 3
Timberland Boots
Timberland Shoes
UGG Boots
UGG Crochet Boot
Prada Shoes
Prada High
Prada Leather Shoes
Gucci Shoes
Gucci High
Gucci Leather Shoes
Dolce Gabbana
DG Leather Shoes
Lacoste Shoes
Ice Cream Shoes

Nike Air Max 87
Nike Air Max 88
Nike Air Max 90
Nike Air Max 95
Nike Air Max 97
Nike Air Max 180
Nike Air Max 360
Nike Air Max Ltd
Nike Air Max 2003
Nike Air Max 2007
Nike Air Max Tn
Nike Air Max Plus Tn 8
Nike Shox NZ
Nike Shox OZ
Nike Shox VC
Nike Shox R2
Nike Shox R3
Nike Shox R4
Nike Shox R5
Nike Shox TL
Nike Shox TL 3
Nike Shox Bmw
Nike Shox Zoom
Nike Shox Rival
Nike Shox Torch
Nike Shox Turbo
Nike Shox Leaper
Nike Shox Flight
Nike Shox Testify
Nike Shox Monster
Nike Shox Classic
Nike Air Jordan 1
Nike Air Jordan 2
Nike Air Jordan 3
Nike Air Jordan 4
Nike Air Jordan 5
Nike Air Jordan 6
Nike Air Jordan 7
Nike Air Jordan 8
Nike Air Jordan 9
Nike Air Jordan 10
Nike Air Jordan 11
Nike Air Jordan 12
Nike Air Jordan 13
Nike Air Jordan 14
Nike Air Jordan 17
Nike Air Jordan 19
Nike Air Jordan 20
Nike Air Jordan 21
Nike Air Jordan 22
Nike Air Jordan 23
Nike Jordan 7.5
Nike Jordan Spizike
Nike Jordan 7 Clear
Nike Jordan Dub Zero
Air Jordan 3 + AF1
Air Jordan 5 + AF1
Air Jordan 12 + AF1
Air Jordan 23 + AF1
Nike Air Dunk
Nike Dunk High
Nike Free 3.0
Nike Free 4.0
Nike Free 5.0
Nike Free 7.0
Nike Lebron James
Nike James Lebron 3
Nike James Lebron 4
Nike Lebron James 5
Nike Lebron Soldier
Nike Zoom Lebron Low
Nike Air Force 1
Nike Air Force 25
Nike Air Force One
Nike Air Force 1 High
Nike Air Force 1 Light
Nike Air Force 1 Clear
Nike Air Force 1 Supreme
Nike Air Force 1 Bird's Nest
Nike Air Rift
Nike Air Stab 89
Nike Air Foamposite
Nike Bird's Nest
Nike Football Shoes
Nike Zoom Kobe
Nike Zoom
Nike Shoes
Bape Sta
Bape Star
Bape Sta Air
Bape Sta High
Bape Star Logo
Bape Star Clear
Adidas Shoes
Adidas T-Mac
Adidas Samba
Adidas Dragon
Adidas Gazelle
Adidas Garnett
Adidas Country
Adidas adiPRENE
Adidas Gil Zero
Adidas Adicolor
Adidas NBA Shoes
Adidas Good Year
Adidas Climacool
Adidas Stan Smith
Adidas Bird's Nest
Adidas City Series
Adidas Superstar 35Th
Adidas Beijing 2008
Adidas Football shoes
Puma Shoes
Puma Osu Shoes
Puma Ferrari Shoes
Puma Fluxion Shoes
Puma Running Shoes
Puma Bmw Sauber F1 Team
Converse Shoes
Converse All Star
Converse One Star
Converse High
Converse Wade 1 2 3
Timberland Boots
Timberland Shoes
UGG Boots
UGG Crochet Boot
Prada Shoes
Prada High
Prada Leather Shoes
Gucci Shoes
Gucci High
Gucci Leather Shoes
Dolce Gabbana
DG Leather Shoes
Lacoste Shoes
Ice Cream Shoes