More zoom viewer experiments (see previous post), this time with a linked map that updates as you browse the tree (SVG-capable browser required). As you browse the frog classification the map updates to show the location of georeferenced sequences in GenBank from the taxa in the part of the tree you are looking at. The map is limited to not more than 200 localities, and many frog sequences aren't georeferenced, but it's a fun way to combine classification and geography. You can try it at:
http://iphylo.org/~rpage/deeptree/7.html
or watch the video:
"On my desk by Sunday Afternoon"
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Several web-media have covered the story of the impending appearance of an updated list of items missing from the Egyptian Museum in Cairo after the events of 28th January 2011. There has been a leaked version of dubious authenticity circulating. This indicates the number of items that we should have been looking out for on the international antiquities market over the past weeks as numbered in the hundreds, rather than tens. The report was due to be published on Sunday, but has still not appeared.The reason is not far to seek, its compilation was required by the Minister of Antiquities Affairs, Zahi Hawass… who by Sunday was no longer the Minister. It seems the Museum is not only unable in the space of some five weeks to produce even a list – let alone photos of the missing objects, but even sees no need to do so when there is not somebody like Hawass inciting them to do their job. Because accounting for what has happened to the cultural items under their care is precisely what their job consists of. Surely at the basis of any collection is proper documentation. The world is looking on with continuing dismay as each day passes without any information and wondering just what kind of documentation this long established museum collection actually has. Whatever type it is, it is obviously inadequate to the task in hand.
How many other modern measures put in place by the former Head of the SCA and Minister of Antiquities have similarly gone by the board while waiting for the current political uncertainty to resolve itself?
The Mendeley API Binary Battle - win $US 10,001
Now we'll bring the awesome. Mendeley have announced The Mendeley API Binary Battle, with a first prize of $US 10,0001, and some very high-profile judges (Juan Enriquez, Tim O'Reilly, James Powell, Werner Vogels, and John Wilbanks). Deadline for submission is August 31st 2011, with the results announced in October.
The criterion for judging are:
Start your engines...
The criterion for judging are:
- How active is your application? We’ll look at your API key usage.
- How viral is the app? We’ll look at the number of sign ups on Mendeley and/or your application, and we’ll also have an eye on Twitter.
- Does the application increase collaboration and/or transparency? We’ll look at how much your application contributes to making science more open.
- How cool is your app? Does it make our jaws drop? Is it the most fun that you can have with your pants on? Is it making use of Facebook, Twitter, etc.?
- The Binary Battle is open to apps built previous to this announcement.
Start your engines...
Nomenclator Zoologicus meets Biodiversity Heritage Library: linking names directly to literature
Following on from my previous post on microcitations I've blasted all the citations in Nomenclator Zoologicus through my microcitation service and created a simple web site where these results can be browsed.
The web site is here: http://iphylo.org/~rpage/nz/.
To create it I've taken a file dump of Nomenclator Zoologicus provided by Dave Remsen and run all the citations through the microcitation service, storing the results in a simple database. You can search by genus name, author and year, or publication. The search is pretty crude, and in the case of publications can be a bit hit and miss. Citations in Nomenclator Zoologicus are stored as strings, so I've used some crude rules to try and extract the publication name from the rest of the details (such as page numbering).
To get started, you can look at names published by published by Distant in 1910, which you can see below:
If the citation has been found you can click on the
icon to view the page in a popup, like this:
You can also click on the page number to be taken to that page in BHL.
I've also added some other links, such as to the name in the Index to Organism Names, as well as bibliographic identifiers such as DOIs, Handles, and links to JSTOR and CiNii.
So far only 10% of Nomenclator Zoologicus records have a match in BHL, which is slightly depressing. Browsing through there are some obvious gaps where my parser clearly failed, typically where multiple pages are included in the citation, or the citation has some additional comments. These could be fixed. There are also cases where the OCR text is so mangled that a match has been rejected because the genus name and text were too different.
This has been hastily assembled, but it's one vision of a simple service where we can go from genus name to being able to see the original publication of that name. There are other things we could do with this mapping, such as enabling BHL to tell users that the reference they are looking at is the original source of a particular name, and enabling services that use BHL content (such as EOL and Atlas of Living Australia to flag which reference in BHL is the one that matters in terms of nomenclature.
The web site is here: http://iphylo.org/~rpage/nz/.
To create it I've taken a file dump of Nomenclator Zoologicus provided by Dave Remsen and run all the citations through the microcitation service, storing the results in a simple database. You can search by genus name, author and year, or publication. The search is pretty crude, and in the case of publications can be a bit hit and miss. Citations in Nomenclator Zoologicus are stored as strings, so I've used some crude rules to try and extract the publication name from the rest of the details (such as page numbering).
To get started, you can look at names published by published by Distant in 1910, which you can see below:
If the citation has been found you can click on the
icon to view the page in a popup, like this:
You can also click on the page number to be taken to that page in BHL.
I've also added some other links, such as to the name in the Index to Organism Names, as well as bibliographic identifiers such as DOIs, Handles, and links to JSTOR and CiNii.
So far only 10% of Nomenclator Zoologicus records have a match in BHL, which is slightly depressing. Browsing through there are some obvious gaps where my parser clearly failed, typically where multiple pages are included in the citation, or the citation has some additional comments. These could be fixed. There are also cases where the OCR text is so mangled that a match has been rejected because the genus name and text were too different.
This has been hastily assembled, but it's one vision of a simple service where we can go from genus name to being able to see the original publication of that name. There are other things we could do with this mapping, such as enabling BHL to tell users that the reference they are looking at is the original source of a particular name, and enabling services that use BHL content (such as EOL and Atlas of Living Australia to flag which reference in BHL is the one that matters in terms of nomenclature.
New Minister for Culture and Antiquities in Egypt
Dr. Emad Abu Ghazi, professor of archival studies at Cairo University ( a Medievalist it seems) will be new Minister of Culture and antiquities in Egypt, replacing the SCA and the recently formed Ministry of Antiquity Affairs . It seems that within the Ministry the SCA will be recreated (or retained) – so a return to the pattern of all but the last few days of the Muarak era. It is currently being reported by apparently reliable sources in Egypt that it will be headed by Dr Abdel (Mohamed Abdel) Maqsoud, former head of Alexandria and Lower Egypt under Hawass. He has been in the news recently for shipping the entire contents of the compromised Qantara storerooms under military escort to Cairo. If this is true, let us see whether his appointment results in any changes in the model of doing things created by his former boss Zahi Hawass.
The situation of archaeology in the state administrative and legislative systems is crucial to its ability to effectively protect the archaeological resource from unmitigated damage. The name of the new ministry is interesting, though it is difficult at this stage to decide whether it is one to be excited about or apprehensive about. In former days, the Supreme Council of Antiquities came under the Ministry of Culture, which gave rise to the problem (not restricted by any means to Egypt alone – see the UK for example) that archaeology was financed from a common pool of funds which had to be divided among other areas of culture. Opera and brass bands for example. In a case like Egypt, where “archaeology” (in a broader sense) contributes funds, many of them end up being siphoned off to support those that do not, opera and brass bands for example, and not being ploughed back into archaeology.
But of course what is generating the revenue is not “archaeology” itself, but tourism. If there are tourists around, where there are standing ruins or romantic looking humps and bumps in a field, given the appropriate marketing, infrastructure and presentation – you can make money out of them. Hawass was one of the ones who understood the point about “presentation”, having done a great deal to open eyes in his country to how sites SHOULD look if you want the tourists to not turn away in disgust from all but the most iconic of sites.
From the point of view of archaeology, the creation of a Ministry for Antiquities Affairs was a positive step forward with the potential of giving it some independence, not only financial but also of state cultural policy. This would, potentially at least, allow the creation of policies more likely benefitiing the archaeological record and its conservation and better management.
The problem with the former model of seeing everything under the 'promoting tourism' model is that the sites that attract tourists are only part of the archaeological record. The finds visitors want to see in museums fall into strictly definale groups (see teh UK Treasure Act). A well-preserved upper Palaeolithic kill site, or the complex of waste dumps of a nineteenth century glassworks or the soil stains of a decayed medieval peasant hovel on the site where some tycoon wants to build a supermarket (“creating local jobs”) for example are not tourist attractions. But it is precisely such sites that need to be seen as just as much part of the archaeological heritage as a Karnak (or Carnac) or KV62 (that’s Tut’s tomb for the rest of us). Its these sites which need to be protected from needless and unmitigated destruction, not just those that tourists pay through the nose to visit.
So what is behind this new title? What are these antiquities it covers? Is an undisturbed scatter of Upper Palaeolithic flints on the desert surface an “antiquity” for everyone (including Egypt’s current military lawmakers)? Or are “antiquities” the shattered visage half-sunken in the sand of Shelley’s Ozymandias King of Kings (30 Egyptian pounds adults entry fee)? Is the juxtaposition of antiquities and culture intended to convey that these (yet-to-be-defined) antiquities are something separate from culture (“and”) or does the term culture include them? Will antiquities be treated in the New Egypt as a separate entity, or as part of a broader understood cultural heritage – and whatever the answer, is that a good or bad thing?One thing is clear, in the near-immediate dissolution of the newly-formed ministry (just) for antiquities, in a sense, the position of archaeological resource management has already been weakened with a few days of the beginning of the process of creating a “new Egypt”.
UPDATE 6 3 11: Well, it seems that, more than usual, one hand does not seem to know what the other is doing in the transitional government (using the term loosely) . Kate Phizackerley has published another version of the same events… Hawass' Successor to be Elected?. Of course, all the time while there is this dithering about policy and politics and in-fighting of nterest groups, the antiquities are suffering. Let us hope that an effective system of protection is up and running as soon as possible.
UPDATE 14.03.11: It turns out my "well-informed source" was wrong and the new appointee as the Minister for Antiquities is (it is now being reported!) Prof. Dr. Alaa El-Din Shaheen (apparently his name is transliterated in a variety of ways)
Where do You Stand on the Issue of Looting?
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Zahi Hawass gives his reasons for resigning and reminds us of a fundamental truth, as an archaeologist in the current situation in Egypt he is unable to ensure the protection of the country’s antiquities from looting, vandalism and theft. The pressing need to work effectively for the protection of the archaeological record wherever possible from destructive exploitation should be at the forefront of the mind of every concerned archaeologist everywhere. Zahi Hawass has many loud critics in archaeological circles in Europe and North America, but somehow I cannot see any archaeologists there in protest about being unable to stop the commercial exploitation of the archaeological record. In Great Britain archaeologists call artefact hunters destructively selectively extracting all the “collectables” out of the accessible archaeological sites of the nation their “partners”. I do not see many of my British colleagues taking any sort of moral stand whatsoever on this erosion of the finite resource. Hawass did.
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