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PAGES endorses Neotoma

PAGES has endorsed Neotoma as a recommended data resource and repository for Quaternary paleoecological and paleoenvironmental data.  Neotoma joins NOAA/NCEI Paleoclimatology and PANGAEA as recommended data depositories.  For more information, see PAGES Data Guidelines
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Posted by Jack Williams on 01/23

Neotoma Newsletter 2017

Dear Neotoma Members,

This short end-of-year newsletter is intended to highlight a few accomplishments and look ahead.  Because everyone is busy, we've focused on a few highlights rather than a comprehensive list of everyone's many(!) accomplishments. 

One quick request to all:  If you know of colleagues who might be interested in joining Neotoma as members or contributing data, please consider reaching out to them. We seek to grow the Neotoma community and make it open to all interested scientists.
*Joining Neotoma as a memberhttps://tinyurl.com/NeotomaMember
*Contributing data:  To get started, talk to a Data Steward or go to: https://www.neotomadb.org/data/category/contribution

Highlight Accomplishments for 2017
*Neotoma vision paper accepted by Quaternary Research, with a publication date of early 2018.  A copy of proofs is available here

*Neotoma accredited by ICSU-WDS  This year Neotoma became a member of the World Data System (https://www.icsu-wds.org/), a global, interdisciplinary, accreditation body for data providers, and data service providers.  This accreditation ensures that Neotoma is part of a body of global experts, continually working toward best practices in data management, storage and access.

*Mona Dombosh, Vertebrate Data Steward, joins the team!  Mona will be uploading FAUNMAP2 and MIOMAP data.  She and Allison Stegner joined Eric Grimm for an intensive training workshop in late October and uploaded a number of datasets during that time.  Ed Davis has developed scripts to batch-export data from FAUNMAP2 into Tilia files, ready for cleaning and upload, and will be working on the MIOMAP port in early 2018.

*EPD Data uploads going strong!  Thomas Gisecke, Pietr Kunes, Eric Grimm, and others met in November for an intensive EPD Steward training workshop.  Since then, several EPD datasets are being uploaded daily.  It's a lot of fun checking the Neotoma home page (www.neotomadb.org) and seeing all the new datasets going up.  You can follow updates from the EPD team on Twitter at @EuPolDB

*First organic biomarker dataset has been uploaded. In February 2018, Jonathan Nichols is hosting a workshop, co-sponsored by the EarthCube C4P project, to train organic geochemists in the Tilia interface and begin uploading new records to Neotoma. 

*New funding from NSF-EarthCube to the Throughput project (PI: Simon Goring) to begin developing standards for ecological and geological data and to the Geochron-API project (PI: Brad Singer) to begin developing systems that would let geochronology labs post their data to online servers, for use by third-party resources such as Neotoma.

*First elections held for the Neotoma Leadership Council!  This is a major milestone as we establish the Neotoma Leadership Council as the primary policy and governing body for the Neotoma Paleoecology Database.  Welcome to Dr. Suzie Pilaar-Birch as the newest member of the NLC!

Major Goals for 2018

*Porting of Neotoma DB from Windows/SQLServer to Linux/PostGresSQL.  The CEI team (Mike Stryker and Steve Crawford) are making excellent progress and we anticipate completion in the first quarter of 2018.  This back-end update will streamline the administration of Neotoma (currently, the website is on a Windows server and database on a Windows server), reduce costs, and facilitate third-party development by moving to an open-source software system.

*Embargo Manager.  This is next in the development queue after we finish the Windows to Linux port.  Our goal is to enable scientists to upload data to Neotoma prior to publication, enabling to use Neotoma's full functionality, and then quickly release their data upon publication.

*Building Partnerships with Professional Societies.  We are in the process of reaching out to InQua, PAGES, AmQua, SVP, and other professional societies to gain recognition for Neotoma as a recommended and trusted data resource.

*Surface sample dataset uploads for ostracodes and testate amoebae.  Both the ostracode and testate amoebae working groups (Stewards: Brandon Curry, Allison Smith, Bob Booth) have been preparing and cleaning Tilia files for data uploads.  Everything is well positioned for a wave of data uploads in 2018.

*Workshops.  Neotoma, the Palebiology Database, and iDigPaleo (via grants Earth-Life Consortium and ePANDDA) will be hosting a Data Derby workshop in May 2018, for interested users of the new programmatic tools that can jointly search Neotoma and Paleobiology Database resources.

This short email skims past many other accomplishments in 2017: ongoing uploads of diatom, ostracode, pollen, and testate amoebae data; ostracode and IBS workshops; extension of Stratigraphic Diagrammer to show vertebrate data; development of a system for generating DOIs for Neotoma data; partnership with the NSF EarthRates RCN to establish community needs and priorities for the coming years.  Lots of progress on lots of fronts, thanks to hard work by a lot of people!  

So, deepest thanks to all, and best wishes for 2018. 

Neotoma Executive Working Group
Jack Williams
Jessica Blois
Alison Smith
Eric Grimm


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Posted by Jack Williams on 12/22

Neotoma Elections: 2017 Leadership Council

Thanks to those who voted for the next round of Leadership Council members, and thanks to the nominees for their willingness to serve.  43% of Neotoma members responded, to fill 4 spots on the Leadership Council.  The top four vote getters were Eric Grimm, Suzanne Pilaar Birch, Don Charles, and Thomas Giesecke.  All four will serve a new 4 year term, from 2018-2021.
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Posted by Jack Williams on 12/22

Neotoma accredited by ICSU-WDS

Neotoma has joined the ICSU World Data System as a Regular Member.  ICSU-WDS certification follows a rigorous peer-review process and recognizes Neotoma as a trusted data resource for paleoecological, paleoenvironmental, and associated data.
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Posted by Jack Williams on 09/19

Latin American data from the University of Amsterdam

The University of Amsterdam has a long history of paleoecological research in northern Latin America, beginning in the 1960s with the pioneering research of Thomas van der Hammen and continued by Henry Hooghiemstra, who along with their students, postdocs, and colleagues generated hundreds of papers and a large quantity of data over the past 60 years. A major push is now being made to upload these data to Neotoma/Latin American Pollen Database with funding from NWO (Nederlandse Organisatie voor Wetenschappelijk Onderzoek – Netherlands Organisation for Scientific Research) and DANS (Data Archiving and Networked Services). A recent article in Geo.Brief describes this effort (in Dutch).
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Posted by Eric Grimm on 05/24

Cyberinfrastructure in the Paleosciences: A 10-Year Vision

Just posted to Authorea: Cyberinfrastructure in the Paleosciences: Mobilizing Long-Tail Data, Building Distributed Community Infrastructure, Empowering Individual Geoscientists.  This, written in response to NSF CI 2030 planning and Dear Colleague Letter 17-031.   This document describes our vision for cyberinfrastructure needs in the paleogeosciences over the next 10 years.  The Authorea version is open to comments for at least the end of April, 2017.  Comments welcome!
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Posted by Jack Williams on 04/07

Stratigraphic Diagrammer extended to ostracodes and diatoms

Neotoma's Stratigraphic Diagrammer, available through Explorer, now will display stratigraphic diagrams for diatoms and ostracodes.  (The previous version had worked only for pollen data).  The next planned extension is for vertebrate data.

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Posted by Jack Williams on 01/26

Neotoma accessible via the new NOAA-NCEI Paleo Data Search

Neotoma accessible via the new NOAA-NCEI Paleo Data Search


NOAA-NCEI and the World Data Service for Paleoclimatology have initiated a new web-based Search application. The application provides improved search and download capabilities via a graphical user interface (GUI), plus a web service (including API) allowing users to obtain dataset metadata in XML or JSON format.  The user can choose to search across one or many archives and data publishers, including Neotoma. The web service URL is: https://www.ncdc.noaa.gov/paleo-search and will soon replace the existing Search capabilities on the NOAA/WDC Paleoclimatology website.

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Posted by Eric Grimm on 01/06

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