Paleomaps: SDI for paleoenvironment GIS data
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Willmes, Christian
Becker, Daniel
Verheul, Jan
Yener, Yasa
Zickel, Mirijam
Bolten, Andreas
Bubenzer, Olaf
Bareth, Georg
Paleoenvironmental studies and according information (data) are abundantly pub-lished and available in the scientific record. However, GIS-based paleoenviron-mental information and datasets are comparably rare. Here, we present an OpenScience approach for collecting and creating GIS-based data and maps of paleoenvironments, and publishing them in a web based Spatial Data Infrastructure (SDI),for access by the archaeology and paleoenvironment communities. The Open Science approach to the publication of data, allows to properly cite the publisheddatasets as bibliographic sources in research that builds upon these data sets.This paper has its focus on the implementation and setup of the Free and OpenSource Software for Geospatial (FOSS4G) based SDI, and on the workflow forcompiling and publishing the GIS data.
 you right so we're just getting started and this is the final presentation for this session so that will cue the door going up there. So Christian's going to talk about Paleo Maps SDI for Paleo Environment GIS data. Thank you very much. Yes, I'm from University of Cologne directly here, not even 50 km north of Bonn. And yeah, we'll talk about the project we developed out of a project I'm working in for, yeah, what I do since some years. And this project I'm working in since some years is called the Collaborative Research Center 806. This is an interdisciplinary research project out of the disciplines of archaeology, the geosciences and cultural sciences that investigates the question of how anatomically modern humans, homo sapiens, yeah, dispersed or migrated through the world and in particular from this research scope into Central Europe. And this project runs since 2010 and no, since 2009 and we are funded until summer 17, so that's then eight years. Maybe we get an extension for even four more years, that would be 2021. And if you are curious about it, you can get more information under this URL about the whole research project. So I'm in this research project with about 80 scientists working there. I'm responsible for the data management. So I'm the GIS guy and also technical guy. I've since 2010 I'm working there and I built this infrastructure called the Collaborative Research Center 806 database for managing the research outputs of this project. And yeah, I do this with some student assistants and yeah, it's a quite small team, but we have a nice website. You can visit it. The URL is given here. It has several different data catalogs and STI interface. We built on GeoNode technology for the metadata of the non geospatial data. We have a CCAN instance running. Then we have a file based back end for large data files that are not going into the relational databases and the infrastructure itself is based on type of three content management system and we developed several extensions for it to handle the different scope of the infrastructure. And yeah, out of this we faced often the request for providing GIS data for the archaeologists in the project to basically build maps to present the data in a paleo environment context. And so we got a pile of paleo environmental GIS data we had and we just thought why don't we share it with a wider community. And yeah, so we came up with this more or less sub project of this data management project where we, yeah, so you might think we have lots of different sources for paleo environmental information. So we have a lot of different sources of information in the published record, but very few GIS based sources for paleo environmental information. So our workflow is we, okay, we'll detail in the next we have this four main different sources of this paleo environmental information that would be I organized it along two axes, which is the first axis is data representation. If it's unstructured or structured information, or the spatial information if it's an intrinsic spatial information of the data or it's an annotated I call it. I'm not sure of this term. I just came up for this project a half a year ago. So it's in the works. So basically we have like published papers with text where it's written okay we had tear glaciers and they were the river Rhine 2000 200,000 years ago when this and this way just in plain text and we can somehow model it in a GIS data set from this information. Then we have like structured texture non GIS directly not not directly GIS data in your like for archaeologists they often have big Excel spreadsheets with tons of artifacts and yeah so this kind of informations. And then we have like maps for for published in books or as maps so we scan them and georeference them and have them in the STI and some few GIS based data sources. There are luckily some quite good poly environmental data modeling projects going on. They're using the same climate models like the IPCC use for climate forecasting. They apply it to these models to poly environmental conditions like what you can get from ice course you can get the concentrations of several greenhouse gases and yeah the the orbit parameters of the Earth and the solar radiation are just physical equations. You can input in these models and then you can come up with quite good models of these poly environmental times and we can use that too. So this is how it looks like this is the maps I spoke of some examples. There's like the textual informations from some publications we put this different kinds of informations into we'll talk about this in a few seconds. Then we have this GIS data sets is different. That are available and the other like relational databases spreadsheets and strike other structured files like XML or C3. So we have a collaborative database we use internally only for storing this information sources and handling them and querying them. So our yeah organization organization platform and from this we create these GIS data sets that we then publish on the website I showed before and this is what the STI part looks like. We have the GeoNode for some larger data sets we have still a map server running because we had the map server before we used GeoNode. We still have it running for some data sets and we have a map proxy for mainly caching external services which we also provide through our front end. But also to to cache for example the base layer because it's just way faster than the Geo server in here. And yeah some we have it all within the university local area network so it's not vulnerable to hackers and we send it either through the web front end which is then the proxy or we proxy the WMS WFS etc. Through a simple PHP reverse proxy to send the contents just just against hackers. Because you don't think it but there are some people who enjoy to compromise small academic projects for no reason. I don't get it but you need this kind of measures somehow. So this is what it looks like I can even try to show it online I linked it. It's loads in the. Yeah. So you just an example data sets. This is a catalog you can search and then we have like you know it from each GS catalog is. So standard spatial data infrastructure but integrated from. We developed a custom type of three extension to integrate the GeoNode. Here into our website design GeoNode has a rest API so we talk to this rest API and. Include here this is plain GeoNode functionality but in another design just you know a front end. So this is what the data catalog looks like with a different sources you have several filters and. Yeah can search through it. I'm quite. How to see say. I quite like the search functionality we have for example. It looks like this it's. So it searches in different spaces and the GM is an abbreviation for it. Last glacial maximum and you see directly what kind of people are connected to it what maps we have what data sets we have. We could then. Go and see some data set. This is loading so this is what the data set would look like there's several. Different resources on it. Like another map we can then load. So. Okay you got me as some zoom bug but. So. Yeah this is what the infrastructure. Looks like. And. Yeah we also. Aimed to implement all these. Concepts of open science and open data. And. Yeah. Open sharing of this data sometimes we have some. Other. Me myself don't have these issues but there are some issues with. Copyright for this data underlying from it because when we get it from published sources. And reuse it just. Yeah we can do it because we say it's a scientific work we built a new data set from it. So we published it published it like a scientific resource in our database using a DOI digital object identifier. To have it cited like this in your publication. If you use it for example for as a base map for archaeological finds. Pretty nice you can just tell us and we get some. Credits or impact from it and to solve this problem with this. Copyright issues so it's basically in science it's a CC by you have to site your sources of course so that we. Facilitate this by having this standardized. Document around like such a data product this data set for the LGM map. We cite all the sources we used here described how we built this data set. In this is. Not yet fully automated because. Point one is we need to write this text ourselves of course no computer can do it or. We are not capable to tell the computer how to do it and. Yeah we we just can have this metadata be included in this large test template and then fill out our. Describing text additionally to it and have it then. Published a come with this data. Again this already it maybe was a bit fast but yeah thank you. That just means there's lots of times for questions. Someone down here had a question. I think it will work like this. Okay. Okay. So thank you for the presentation working kind of in a similar setup it's in historical science so my question is not so much. Ask from the viewpoint of the SDI but more from the user feedback because where I come from. You know we start out this project you know and people come to us and say that okay I have this lots of data and they come and they give us like a. Like a Microsoft Office document so it's obviously kind of hard to process that kind of data and also. It's well the idea of putting it on a permissive license is not that popular to state it in a more defensive way so my question is how do the actual scientists reacted at because I don't know how the paleo community is. Yeah. Equipment that kind of skill set that's the first part and the other part with attitudes towards permissive licenses so that would be my question. Thank you. Thank you. Thank you. Thank you. Yes, yes I have exactly the same problems. None of the scientists is really not known but very few are thinking about this at all and yeah we are not really. Yeah we we we can come mostly up with our own ideas to provide data sets to them so giving them to use because we get paid for it but they're not often come to us for asking something. So we haven't but we collaborate in it and almost never they want to publish the data just for publishing it and sharing it. It's the other way around they're really really frightened of their colleagues or their concurrence to get their ideas and publish it before they do it. So they would not share it before they really exploited all of it and this never the case so they don't share it if they don't have to the funder the German research foundations forces them to publish their research results after the project ends for at least 10 years. After the project funding ended it must be available so that's why this platform is funded and they have to publish their documents but they come as you said with a Microsoft Office document. A table in the Word document or a PDF and say OK this is I did my duty. Yes my data and then they have even the option to say I just don't want to have it publicly they are just on request so. Users interested people who want to have access to the data can press a button to request access and the data set owner and we get information that there is an interest and the data set owner can. Has sent to argue which is then locked in our system so you can ask yeah why do you want it and then he can say no it's not of your interest and something like this but in this is not really often the case so. Much of it also goes around our infrastructure they often just they contact them directly by email and they talk about it we have like maybe one request a month from external entities to some data set so it's not so much. So we have also the visitor statistics are like. 30 visits a day so it's a really low traffic some website but. So. Yeah. But yeah we. We came up with this project and we also get some good feedback from this we just have it since the half a year this. Providing of polyenvironmental GS data sets and there are some first code science that this might be. Will increase the use of the infrastructure. I hope so. To hear just go. Thank you thanks for the talk. Maybe I missed it but are you also able to query directly on the data you have or is it mainly a platform to just. Disperse your data. Sorry yes. So we have. We have a metadata according to each data set and for the spatial data sets we. Query the. Geo node rest RP endpoint with the same geo node internal search I think it's a full text search on the metadata items. And on the pure data set side we have the secan endpoint and there is an elastic search endpoint for this. The metadata items and we have some filters like for the we have these. Seven yeah. Research classes in our project which you can then browse for their data set items they have in the infrastructure or you can use. A map for spatial browsing data sets so you can give an extent or location for data set for which you can browse then we have tax you can filter along. You can't query the data directly like for instance fire of a query which has given me all records from some plant species in the young dryers. You. Let's say you have some not only metadata but also real data queryable in the in your database. Can can you really query the data so give me all the upper level young dryers plants. Yes when I started this project this was my aim after some years I. Yeah. How to say. Did not. Proceeded with this aim because I saw this. Just too much for one person and three student assistants to get this done in any. Making sense way we have this internal. Media Wiki with which facilitates some of it. Better than the. This infrastructure but this is. The box of Pandora if you do it so you need the big stuff like hundreds of people to do it good. So. That's why we didn't implement it. Not enough resource. Did you have a follow up. Yeah it was a great time I really enjoyed it. I love the idea of giving map data at DOI. I just wish that had been there when I was publishing data. The question I had was if you go back one slide again to your media Wiki page. That one yes when you feed your external literature and do you hand extract the locations and such like or can you do that automatically yet. No it's. It goes something like this some someone says I found this publication this is so interesting information in it about this and that and then. We take the bibliographical information put it into our system and then we add some additional information we can grasp from it or the the domain scientists expert tells us what it's valuable from there and we just. Yeah take like which time slice it's concerns which spatial extent which environmental variables are given or which architect archaeological cultures are present and stuff like this. But yeah it's really laborious tax work and yeah even if you had tens of students working on it for free which we don't have that would not be enough it's not never enough so. So anything else. So anything else yep. Thank you once again. I was wondering how you managed to get along with more flexible data models that actually change with. With the interest of each researcher because that's what I figured that's kind of hard to represent especially in a relational database. So perhaps you could describe the challenges in that kind of area. Yes the data modeling is really the the hard part which is not so seen from the outside this is what this also is the most work which I have to think about. And in this media VK instance I have the data this is more less my data model which is all the time extended and adopted. So we have. Like for the cultural context. Class it's called in there yeah different attributes and I always work on refining them and adapting them. Luckily this this software is really flexible to this so I just have to change one point and it's depth to. The rest of the system this in a relational database. Also this is really like a test of web to go and you don't have to deal with like command line SQL queries and. To be honest it's too easy to destroy your SQL database if you don't backup then with some queries and so I stick to this and do it not directly on the relational database for the data model. Adapting because it's just proof to be. Yeah more resilient in some way to to errors and let's just you can revert every change it's locked and. And yeah but this is really the hard part to the data modeling. So my aim was when I started out to develop the ontology and publish it and get it standardized and all this stuff. This all went down along the way it's too hard for one person. There there are some standards from archaeology community like the sea doc CRM is really well known. Geospatial standards of course and there would this would be a combination of different vocabularies integrated into on domain ontology for this project. I have this in some way it's implemented it's there but it's not formalized. I could do it maybe for some publication if I have some time I could try to formalize it. So I just finished my PhD in May so I have to publish my dissertation still but I did not went so far in this PhD to formalize all of it. So I'm concerned on several specific topics in there. So. Okay I think it's coffee time so thank you again Christian for the presentation. Thank you.
 you  right so we're just getting started and this is the final presentation for this session so that will cue the door going up there.  So Christian's going to talk about Paleo Maps SDI for Paleo Environment GIS data.  Thank you very much. Yes, I'm from University of Cologne directly here, not even 50 km north of Bonn.  And yeah, we'll talk about the project we developed out of a project I'm working in for, yeah, what I do since some years.  And this project I'm working in since some years is called the Collaborative Research Center 806.  This is an interdisciplinary research project out of the disciplines of archaeology, the geosciences and cultural sciences that investigates the question of how  anatomically modern humans, homo sapiens, yeah, dispersed or migrated through the world and in particular from this research scope into Central Europe.  And this project runs since 2010 and no, since 2009 and we are funded until summer 17, so that's then eight years.  Maybe we get an extension for even four more years, that would be 2021.  And if you are curious about it, you can get more information under this URL about the whole research project.  So I'm in this research project with about 80 scientists working there.  I'm responsible for the data management.  So I'm the GIS guy and also technical guy. I've since 2010 I'm working there and I built this infrastructure called the Collaborative Research Center 806 database for managing the research outputs of this project.  And yeah, I do this with some student assistants and yeah, it's a quite small team, but we have a nice website.  You can visit it. The URL is given here.  It has several different data catalogs and STI interface. We built on GeoNode technology for the metadata of the non geospatial data.  We have a CCAN instance running.  Then we have a file based back end for large data files that are not going into the relational databases and the infrastructure itself is based on type of three content management system and we developed several extensions for it to handle the different scope of the infrastructure.  And yeah, out of this we faced often the request for providing GIS data for the archaeologists in the project to basically build maps to present the data in a paleo environment context.  And so we got a pile of paleo environmental GIS data we had and we just thought why don't we share it with a wider community.  And yeah, so we came up with this more or less sub project of this data management project where we, yeah, so you might think we have lots of different sources for paleo environmental information.  So we have a lot of different sources of information in the published record, but very few GIS based sources for paleo environmental information.  So our workflow is we, okay, we'll detail in the next we have this four main different sources of this paleo environmental information that would be I organized it along two axes, which is the first axis is data representation.  If it's unstructured or structured information, or the spatial information if it's an intrinsic spatial information of the data or it's an annotated I call it.  I'm not sure of this term.  I just came up for this project a half a year ago.  So it's in the works.  So basically we have like published papers with text where it's written okay we had tear glaciers and they were the river Rhine 2000 200,000 years ago when this and this way just in plain text and we can somehow model it in a GIS data set from this information.  Then we have like structured texture non GIS directly not not directly GIS data in your like for archaeologists they often have big Excel spreadsheets with tons of artifacts and yeah so this kind of informations.  And then we have like maps for for published in books or as maps so we scan them and georeference them and have them in the STI and some few GIS based data sources.  There are luckily some quite good poly environmental data modeling projects going on. They're using the same climate models like the IPCC use for climate forecasting.  They apply it to these models to poly environmental conditions like what you can get from ice course you can get the concentrations of several greenhouse gases and yeah the the orbit parameters of the Earth and the solar radiation are just physical equations.  You can input in these models and then you can come up with quite good models of these poly environmental times and we can use that too.  So this is how it looks like this is the maps I spoke of some examples.  There's like the textual informations from some publications we put this different kinds of informations into we'll talk about this in a few seconds.  Then we have this GIS data sets is different.  That are available and the other like relational databases spreadsheets and strike other structured files like XML or C3.  So we have a collaborative database we use internally only for storing this information sources and handling them and querying them.  So our yeah organization organization platform and from this we create these GIS data sets that we then publish on the website I showed before and this is what the STI part looks like.  We have the GeoNode for some larger data sets we have still a map server running because we had the map server before we used GeoNode.  We still have it running for some data sets and we have a map proxy for mainly caching external services which we also provide through our front end.  But also to to cache for example the base layer because it's just way faster than the Geo server in here.  And yeah some we have it all within the university local area network so it's not vulnerable to hackers and we send it either through the web front end which is then the proxy or we proxy the WMS WFS etc.  Through a simple PHP reverse proxy to send the contents just just against hackers.  Because you don't think it but there are some people who enjoy to compromise small academic projects for no reason.  I don't get it but you need this kind of measures somehow.  So this is what it looks like I can even try to show it online I linked it.  It's loads in the.  Yeah.  So you just an example data sets.  This is a catalog you can search and then we have like you know it from each GS catalog is.  So standard spatial data infrastructure but integrated from.  We developed a custom type of three extension to integrate the GeoNode.  Here into our website design GeoNode has a rest API so we talk to this rest API and.  Include here this is plain GeoNode functionality but in another design just you know a front end.  So this is what the data catalog looks like with a different sources you have several filters and.  Yeah can search through it.  I'm quite.  How to see say.  I quite like the search functionality we have for example.  It looks like this it's.  So it searches in different spaces and the GM is an abbreviation for it.  Last glacial maximum and you see directly what kind of people are connected to it what maps we have what data sets we have.  We could then.  Go and see some data set.  This is loading so this is what the data set would look like there's several.  Different resources on it.  Like another map we can then load.  So.  Okay you got me as some zoom bug but.  So.  Yeah this is what the infrastructure.  Looks like.  And.  Yeah we also.  Aimed to implement all these.  Concepts of open science and open data.  And.  Yeah.  Open sharing of this data sometimes we have some.  Other.  Me myself don't have these issues but there are some issues with.  Copyright for this data underlying from it because when we get it from published sources.  And reuse it just.  Yeah we can do it because we say it's a scientific work we built a new data set from it.  So we published it published it like a scientific resource in our database using a DOI digital object identifier.  To have it cited like this in your publication.  If you use it for example for as a base map for archaeological finds.  Pretty nice you can just tell us and we get some.  Credits or impact from it and to solve this problem with this.  Copyright issues so it's basically in science it's a CC by you have to site your sources of course so that we.  Facilitate this by having this standardized.  Document around like such a data product this data set for the LGM map.  We cite all the sources we used here described how we built this data set.  In this is.  Not yet fully automated because.  Point one is we need to write this text ourselves of course no computer can do it or.  We are not capable to tell the computer how to do it and.  Yeah we we just can have this metadata be included in this large test template and then fill out our.  Describing text additionally to it and have it then.  Published a come with this data.  Again this already it maybe was a bit fast but yeah thank you.  That just means there's lots of times for questions.  Someone down here had a question.  I think it will work like this.  Okay.  Okay.  So thank you for the presentation working kind of in a similar setup it's in historical science so my question is not so much.  Ask from the viewpoint of the SDI but more from the user feedback because where I come from.  You know we start out this project you know and people come to us and say that okay I have this lots of data and they come and they give us like a.  Like a Microsoft Office document so it's obviously kind of hard to process that kind of data and also.  It's well the idea of putting it on a permissive license is not that popular to state it in a more defensive way so my question is how do the actual scientists reacted at because I don't know how the paleo community is.  Yeah.  Equipment that kind of skill set that's the first part and the other part with attitudes towards permissive licenses so that would be my question.  Thank you.  Thank you.  Thank you.  Thank you.  Yes, yes I have exactly the same problems.  None of the scientists is really not known but very few are thinking about this at all and yeah we are not really.  Yeah we we we can come mostly up with our own ideas to provide data sets to them so giving them to use because we get paid for it but they're not often come to us for asking something.  So we haven't but we collaborate in it and almost never they want to publish the data just for publishing it and sharing it.  It's the other way around they're really really frightened of their colleagues or their concurrence to get their ideas and publish it before they do it.  So they would not share it before they really exploited all of it and this never the case so they don't share it if they don't have to the funder the German research foundations forces them to publish their research results after the project ends for at least 10 years.  After the project funding ended it must be available so that's why this platform is funded and they have to publish their documents but they come as you said with a Microsoft Office document.  A table in the Word document or a PDF and say OK this is I did my duty. Yes my data and then they have even the option to say I just don't want to have it publicly they are just on request so.  Users interested people who want to have access to the data can press a button to request access and the data set owner and we get information that there is an interest and the data set owner can.  Has sent to argue which is then locked in our system so you can ask yeah why do you want it and then he can say no it's not of your interest and something like this but in this is not really often the case so.  Much of it also goes around our infrastructure they often just they contact them directly by email and they talk about it we have like maybe one request a month from external entities to some data set so it's not so much.  So we have also the visitor statistics are like.  30 visits a day so it's a really low traffic some website but.  So.  Yeah.  But yeah we.  We came up with this project and we also get some good feedback from this we just have it since the half a year this.  Providing of polyenvironmental GS data sets and there are some first code science that this might be.  Will increase the use of the infrastructure.  I hope so.  To hear just go.  Thank you thanks for the talk.  Maybe I missed it but are you also able to query directly on the data you have or is it mainly a platform to just.  Disperse your data.  Sorry yes.  So we have.  We have a metadata according to each data set and for the spatial data sets we.  Query the.  Geo node rest RP endpoint with the same geo node internal search I think it's a full text search on the metadata items.  And on the pure data set side we have the secan endpoint and there is an elastic search endpoint for this.  The metadata items and we have some filters like for the we have these.  Seven yeah.  Research classes in our project which you can then browse for their data set items they have in the infrastructure or you can use.  A map for spatial browsing data sets so you can give an extent or location for data set for which you can browse then we have tax you can filter along.  You can't query the data directly like for instance fire of a query which has given me all records from some plant species in the young dryers.  You.  Let's say you have some not only metadata but also real data queryable in the in your database.  Can can you really query the data so give me all the upper level young dryers plants.  Yes when I started this project this was my aim after some years I.  Yeah.  How to say.  Did not.  Proceeded with this aim because I saw this.  Just too much for one person and three student assistants to get this done in any.  Making sense way we have this internal.  Media Wiki with which facilitates some of it.  Better than the.  This infrastructure but this is.  The box of Pandora if you do it so you need the big stuff like hundreds of people to do it good.  So.  That's why we didn't implement it.  Not enough resource.  Did you have a follow up.  Yeah it was a great time I really enjoyed it.  I love the idea of giving map data at DOI.  I just wish that had been there when I was publishing data.  The question I had was if you go back one slide again to your media Wiki page.  That one yes when you feed your external literature and do you hand extract the locations and such like or can you do that automatically yet.  No it's.  It goes something like this some someone says I found this publication this is so interesting information in it about this and that and then.  We take the bibliographical information put it into our system and then we add some additional information we can grasp from it or the the domain scientists expert tells us what it's valuable from there and we just.  Yeah take like which time slice it's concerns which spatial extent which environmental variables are given or which architect archaeological cultures are present and stuff like this.  But yeah it's really laborious tax work and yeah even if you had tens of students working on it for free which we don't have that would not be enough it's not never enough so.  So anything else.  So anything else yep.  Thank you once again.  I was wondering how you managed to get along with more flexible data models that actually change with.  With the interest of each researcher because that's what I figured that's kind of hard to represent especially in a relational database.  So perhaps you could describe the challenges in that kind of area.  Yes the data modeling is really the the hard part which is not so seen from the outside this is what this also is the most work which I have to think about.  And in this media VK instance I have the data this is more less my data model which is all the time extended and adopted.  So we have.  Like for the cultural context.  Class it's called in there yeah different attributes and I always work on refining them and adapting them.  Luckily this this software is really flexible to this so I just have to change one point and it's depth to.  The rest of the system this in a relational database.  Also this is really like a test of web to go and you don't have to deal with like command line SQL queries and.  To be honest it's too easy to destroy your SQL database if you don't backup then with some queries and so I stick to this and do it not directly on the relational database for the data model.  Adapting because it's just proof to be.  Yeah more resilient in some way to to errors and let's just you can revert every change it's locked and.  And yeah but this is really the hard part to the data modeling.  So my aim was when I started out to develop the ontology and publish it and get it standardized and all this stuff.  This all went down along the way it's too hard for one person.  There there are some standards from archaeology community like the sea doc CRM is really well known.  Geospatial standards of course and there would this would be a combination of different vocabularies integrated into on domain ontology for this project.  I have this in some way it's implemented it's there but it's not formalized.  I could do it maybe for some publication if I have some time I could try to formalize it.  So I just finished my PhD in May so I have to publish my dissertation still but I did not went so far in this PhD to formalize all of it.  So I'm concerned on several specific topics in there.  So.  Okay I think it's coffee time so thank you again Christian for the presentation.  Thank you.
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