Wednesday, 7 October 2009
A late-night entry
Despite mounting pressure, and days when I feel like my PhD might implode (I hope I'm not the only one who has days like this), this week has been good. Increasingly I have more direction for the upcoming projects and I look forward to the legume project, which seems to be taking off. I am excited about the collaboration with the legume group at Kew, which, I am sure, will be inspirational and interesting. And, of course, I look forward to spending some time in London - I love the city (and everyone speaks a language I understand)! Let's hope it'll all work out.
Thursday, 24 September 2009
fun at the museum
I remember how, as a little girl, I once got to go 'behind the scenes' at Pietermaritzburg's Natural History Museum. All I remember is seeing a (dead and decomposing and very smelly) crocodile in a huge bath being prepared for, well, I'm not sure what, but some museum collection. That's when I first realized that there is more to a museum than just the exhibits. And since then I have been fascinated with what happens behind museum doors.
So, it's been great attending a course at Stockholm's Natural History Museum. Not only did we walk through exhibits on our way to work every morning, but we also had the opportunity to see where the museum personnel work and store their materials. Yesterday we climbed to the roof of the museum - which was fun and a little frightening (I seem to be developing a fear of heights as I grow older!). On our way up we passed the dusty and almost-forgotten collecting materials, still marked, of René Malaise, who was a well-known Swedish entomologist and explorer. Today we walked through the 3million-specimen insect collection and saw, amongst others, type specimens collected by Linnaeus' students. For someody like me, coming from a country with a relatively young history of science, this is exiting stuff!
So, it's been great attending a course at Stockholm's Natural History Museum. Not only did we walk through exhibits on our way to work every morning, but we also had the opportunity to see where the museum personnel work and store their materials. Yesterday we climbed to the roof of the museum - which was fun and a little frightening (I seem to be developing a fear of heights as I grow older!). On our way up we passed the dusty and almost-forgotten collecting materials, still marked, of René Malaise, who was a well-known Swedish entomologist and explorer. Today we walked through the 3million-specimen insect collection and saw, amongst others, type specimens collected by Linnaeus' students. For someody like me, coming from a country with a relatively young history of science, this is exiting stuff!
Wednesday, 23 September 2009
databasing
What I like about this Bioinformatics workshop is that, after all the presentations we heard and the information we have been presented with, we have time to implement what we have learnt. We have three days to work on our projects. The advantage of this is that there is more opportunity to get a grip on the content of the course, and there is opportunity to ask people in the know-how for advice. I know for a fact that, had we not been presented this opportunity, I would have gone home and only gotten round to this work in a few months' time, and, of course, forgotten much! So, at the moment I am learning to use mySQL (another language... sigh). ;) I hope to make good progress on setting up my Fabaceae database before returning to Århus on Friday.
Tuesday, 22 September 2009
uBio
I have been perusing the many websites we have been introduced to. Lots of information and tools are available on these websites, so here I summarize the functions available on uBio (links to all tools provided on the website).
- uBioRSS- RSS feeds can be searched based on taxonomic names, as defined in the Species 2000 and ITIS Catalogue of Life 2007 Annual Checklist
- TaxaToy - plots the number of species discovered over time. This can also be queried according to taxon.
- OntoSpecies - provides links to browse taxonomic trees and provides links to several outside web resources
- LigerCat - Literature and Genomics Resource Catalogue
- Aging Portal -resource providing information on the lifespan and aging of species
- LinkIt - allows the user to retrieve taxonomic names (if I remember correctly, even ones that have been misspelled) from websites. (Apparently this tool is meant to be extended extracting info from pdfs in the future.) If these names are present in one of a number of other reference websites (e.g. nomenclatural websites, GBIF, phylogenetic websites, MorphBank, etc.), a link to these names on these other websites is provided.
- FindIT - taxonomic names are extraced from websites, free text or files that are uplaided (including pdfs). This is great if you want a list of species mentioned in a file/document.
- ParseIT - separates scientific names into their various components. Can be used for outputting in XML format.
- MapIT - All names in a document or website are extracted and... Well, the rest I don't really get. Will try to figure it out.
- CrawlIT - Crwals through a website and all links on that website and returns all the names mentioned there.
- X:ID - allows users to create their own identification keys which can be run over the web or locally.
Monday, 21 September 2009
XML Markups
Monday's session of the Bioinformatics workshop I have been attending and blogging about in the last days was the final formal session of the workshop. Donat Agosti, who heads up Plazi, entitled his talk "Literature & XML: or How to Have More Time to Think".
Before he launched into his presentation, Donat challenged us on our motivations for doing science and the reasons we get funded to do science at all. Regarding the last point, science is usually funded for advancements to be made in our knowledge of the world around us and for humanity. However, if this knowledge is unavailable to the rest of the scientific (or non-scientific, for that matter) world, science is failing what it initially really set out to do. So, Donat made a strong point for making science generally accessible and making use of non-copyrighted resources.
Donat then went on to explain how the information that is available in the written format (e.g. in papers) can be marked up using e.g. XML, and the information in these papers thereby made accessible in an electronic format. So, for example, if you publish about a species, info on its location, its host and a predator may perhaps be included in the manuscript. The words in the paper that describe the location, host and predator of the species could thus be defined as such, and accordingly link a species to a location, host and predator. Imagine a world where this information would be electronically accessible (and prevent us from browsing through paper after paper to look for what we need). I imagine that, in addition to saving us hours of time, it would open the door to a myriad of new ideas and analyses and provide a whole new level of understanding of 'how the world works'.
The major factor preventing large-scale marking up of published information is copyrighting. Only older papers can be marked up without violating copyright information. Currently, the Biodiversity Heritage Library (BHL) is scanning and marking up (for taxon only though) large quantities of old publications. When you visit the website, you can therefore search for a taxon and the scanned publications with page numbers (that are linked) can be accessed. If, e.g. your taxon's info is on pp. 98 of 329 pages in a publication, there is no need to trawl through pages of information to try find your taxon - you can go straight to pp. 98 where the taxon is mentioned.
Donat, together with Guido Sautter, a programmer, then went on to explain how they use GoldenGate Editor to mark up documents to XML. The process they use is somewhat slower than the BHL because it is more thorough. Instead of only marking up taxon names, they mark up other information such as taxonomic treatments, morphology, synonyms, etc. A great deal of the process is automated, so that only little input is needed from people.
Finally, the information that's extracted from publications can be linked to websites such as Zoobank, GenBank, be fed to GBIF, etc. There are a vast varity of options.
Before he launched into his presentation, Donat challenged us on our motivations for doing science and the reasons we get funded to do science at all. Regarding the last point, science is usually funded for advancements to be made in our knowledge of the world around us and for humanity. However, if this knowledge is unavailable to the rest of the scientific (or non-scientific, for that matter) world, science is failing what it initially really set out to do. So, Donat made a strong point for making science generally accessible and making use of non-copyrighted resources.
Donat then went on to explain how the information that is available in the written format (e.g. in papers) can be marked up using e.g. XML, and the information in these papers thereby made accessible in an electronic format. So, for example, if you publish about a species, info on its location, its host and a predator may perhaps be included in the manuscript. The words in the paper that describe the location, host and predator of the species could thus be defined as such, and accordingly link a species to a location, host and predator. Imagine a world where this information would be electronically accessible (and prevent us from browsing through paper after paper to look for what we need). I imagine that, in addition to saving us hours of time, it would open the door to a myriad of new ideas and analyses and provide a whole new level of understanding of 'how the world works'.
The major factor preventing large-scale marking up of published information is copyrighting. Only older papers can be marked up without violating copyright information. Currently, the Biodiversity Heritage Library (BHL) is scanning and marking up (for taxon only though) large quantities of old publications. When you visit the website, you can therefore search for a taxon and the scanned publications with page numbers (that are linked) can be accessed. If, e.g. your taxon's info is on pp. 98 of 329 pages in a publication, there is no need to trawl through pages of information to try find your taxon - you can go straight to pp. 98 where the taxon is mentioned.
Donat, together with Guido Sautter, a programmer, then went on to explain how they use GoldenGate Editor to mark up documents to XML. The process they use is somewhat slower than the BHL because it is more thorough. Instead of only marking up taxon names, they mark up other information such as taxonomic treatments, morphology, synonyms, etc. A great deal of the process is automated, so that only little input is needed from people.
Finally, the information that's extracted from publications can be linked to websites such as Zoobank, GenBank, be fed to GBIF, etc. There are a vast varity of options.
Sunday, 20 September 2009
More backtracking - here is a summary of what was presented on Monday last week.
The workshop was introduced by Torsten Eriksson from Stockholm University. He gave a general introduction to databases (DBs), which I found very useful, as I am only starting to think about setting up DBs. Here are some of the suggestions he made for databasing:
1.) Before you start setting up your DB, decide (as far as possible) what you want to put into your database, 2.) Identify the relationship between objects (including the nature of the relationships - one to many vs. one to one, 3.) Identify the attributes of the objects you want to put into the DB, 4.) Identify unique identifiers for each object (attributes should only be dependent on unique identifiers).
As a good exercise, the basic structure of the DB can be sketched, where objects become tables and attributes become columns in the tables. The data type must be specified for each column, unique IDs are columns that may not be empty and, as the name suggest, must be unique. Relationships are then modelled between tables, using the IDs as 'connectors'.
Torsten also suggested that one use one of the open source software to set up DBs, because they are accessible to everyone everywhere. One suggestion that was made is mySQL. There are also DBs that have been designed specifically for certain purposes, e.g. the ontology DBs mentioned in previous blogs, Specify and MX.
Katja Seltmann (see blog on ontologies below) followed with an introduction to MX as an example of a taxonomic database. It is web-based and the core data object is an operational taxonomic unit (OTU), which means that data can be entered for any taxonomi levels. See more here.
In the afternoon Katja and Torsten co-hosted a tutorial during which we were expected to link up the components of the Darwin Core components. To assist in the set-up of the DB, we downloaded phpMyAdmin, which provides an interface for mySQL and, and is therefore a little easier (particularly in the beginning) than entirely coding a DB. And, even if the DB is created using phpMyAdmin, the sql code is provided, which is a definite advantage. Installation of phpMyAdmin was semi-complicated, as it wouldn't just run in Windows. However, some web-searches resulted in Katja establishing that it may be best to download mySQL and phpMyAdmin together using XAMPP. I have tried phpMyAdmin a little, and it seems relatively intuitive. I hope there'll be time in the next week to further develop my DB.
The workshop was introduced by Torsten Eriksson from Stockholm University. He gave a general introduction to databases (DBs), which I found very useful, as I am only starting to think about setting up DBs. Here are some of the suggestions he made for databasing:
1.) Before you start setting up your DB, decide (as far as possible) what you want to put into your database, 2.) Identify the relationship between objects (including the nature of the relationships - one to many vs. one to one, 3.) Identify the attributes of the objects you want to put into the DB, 4.) Identify unique identifiers for each object (attributes should only be dependent on unique identifiers).
As a good exercise, the basic structure of the DB can be sketched, where objects become tables and attributes become columns in the tables. The data type must be specified for each column, unique IDs are columns that may not be empty and, as the name suggest, must be unique. Relationships are then modelled between tables, using the IDs as 'connectors'.
Torsten also suggested that one use one of the open source software to set up DBs, because they are accessible to everyone everywhere. One suggestion that was made is mySQL. There are also DBs that have been designed specifically for certain purposes, e.g. the ontology DBs mentioned in previous blogs, Specify and MX.
Katja Seltmann (see blog on ontologies below) followed with an introduction to MX as an example of a taxonomic database. It is web-based and the core data object is an operational taxonomic unit (OTU), which means that data can be entered for any taxonomi levels. See more here.
In the afternoon Katja and Torsten co-hosted a tutorial during which we were expected to link up the components of the Darwin Core components. To assist in the set-up of the DB, we downloaded phpMyAdmin, which provides an interface for mySQL and, and is therefore a little easier (particularly in the beginning) than entirely coding a DB. And, even if the DB is created using phpMyAdmin, the sql code is provided, which is a definite advantage. Installation of phpMyAdmin was semi-complicated, as it wouldn't just run in Windows. However, some web-searches resulted in Katja establishing that it may be best to download mySQL and phpMyAdmin together using XAMPP. I have tried phpMyAdmin a little, and it seems relatively intuitive. I hope there'll be time in the next week to further develop my DB.
Morphbank
The other part of Friday´s lecture was Debbie Paul´s Morphbank introduction. Morphbank is a repository for photos of living organisms, which is meant to serve as an aid for species identification. Photos come with a range of metadata, which, I think, could potentially be useful for a variety of other reasons. Data can be uploaded via the web individually or in batch, or, if the identification of the specimen is not to species level, be sent to Morphbank directly. Morphbank is also linked to various other online databases.
I browsed around Morphbank a little and it seems that at this stage the coverage for African species is somewhat sparse. Perhaps a reason to raise awareness amongst African researchers of this resource. Also, could it be possible to link Morphbank to other photographic repositories, such as the West African Plant Database or the Flora of Zimbabwe?
I browsed around Morphbank a little and it seems that at this stage the coverage for African species is somewhat sparse. Perhaps a reason to raise awareness amongst African researchers of this resource. Also, could it be possible to link Morphbank to other photographic repositories, such as the West African Plant Database or the Flora of Zimbabwe?
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