Neon bioarchive: Concept of Operations The neon project, Boulder, co version: 26 May 2017



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NEON Bioarchive: Concept of Operations

The NEON Project, Boulder, CO

Version: 26 May 2017

Table of Contents


1Description 2

1.1Purpose 2

1.2Scope 2

1.3 Applicable Documents 2

1.4Reference Documents 2

1.5Acronyms 2



2NEON Bioarchive Facility 3

2.1Overview 3

2.2Functional Design Features 3

2.3Technical and Operating Requirements 4

2.4Information Management 6

2.5Data Products 7

2.6Roles and Responsibilities 7

2.7Risks and Issues to be Addressed 8



2.8Quality Assurance and Quality Control 9



1Description

1.1Purpose


The purpose of this document is to summarize the concept of operations of the NEON Bioarchive. Major elements of the bioarchive include the coordination of sample shipping and the design of standardized protocols across participating facilities.

1.2Scope


This document applies to all samples collected by the NEON Project at terrestrial and aquatic sites during the 30-year life cycle of the observatory. This includes those associated with the Aquatic Observations System (AOS), Terrestrial Observation System (TOS), and Terrestrial Instrument System (TIS).

1.3 Applicable Documents


AD [01]

NEON.DOC.000001

NEON Observatory Design

AD [02]

NEON.DOC.002652

NEON Level 1, Level 2, and Level 3 Data Products Catalog

1.4Reference Documents


RD [01]

NEON.DOC.000008

NEON Acronym List

RD [02]

NEON.DOC.000243

NEON Glossary of Terms

RD [03]

NEON.DOC.000027

NEON Sample Use Policy

RD [04]

NEON.DOC.000019

NEON Data Use Policy

RD [05]

White Paper

NEON Bioarchive Workshop Summary (15 May 2017)

1.5Acronyms


COTS

Commercial-off-the-shelf

DOI

Digital Objective Identifier

GBIF

Global Biodiversity Information Facility

SPNHC

Society for the Preservation of Natural History Collections

TDWG

Taxonomic Databases Working Group



2NEON Bioarchive Facility

2.1Overview


A key feature of NEON’s science design is to establish a “…curated collection of organisms, key body parts of organisms, and substrates… open to researchers for analysis, both now and in the future as new technologies emerge.” [AD [01], p. 31). What we now call the NEON Bioarchive encompasses aquatic and terrestrial samples and specimens (collectively called samples below) collected during annual sampling at NEON sites – i.e. voucher specimens, whole organisms, tissues, and samples processed for chemistry, disease and genetics. It includes shipping, handling, preservation, storage, and distribution of samples.

The overarching goal of the NEON Bioarchive is to make reference material and replicate samples available to the science and education communities for future research and retrospective studies. The collected samples provide a rich resource for future research efforts, enabling scientists to identify organisms, analyze archived blood and tissue samples for viruses and other pathogens, and perform new isotopic, biogeochemical and microbial analyses on water and soil samples.

The bioarchive will be unique among natural history collections as a result of its spatial and temporal scales. It is intended to provide a record of samples of known provenance linked to contextual meta-data that can be repeatedly used for verification of field observations, archived for new studies, and the application of new analytical techniques and technologies. Samples will be stored in replicate and in a manner that protects against major loss in the event of a catastrophe and allows for destructive analysis.

2.2Functional Design Features


The NEON Bioarchive may be single institution or a small consortium of 3-5 collaborating institutions. In either case, the NEON Bioarchive must encompass the entirety of the NEON Bioarchive requirements as described in the NEON Bioarchive Concept of Operations, and address both near term and long-term needs – i.e., pre-2017 “orphan” samples, samples to be collected during initial operations (FY2017-2018), and samples to be collected in full operations (FY2019 and beyond).

A summary of the major design features follows:



  1. The NEON Bioarchive shall have the capacity to:

  1. Accommodate ~100,000 samples per year for no less than 5 years and up to 30 years

  2. Grow as samples accumulate over time

  3. Handle a wide variety of sample types and storage conditions (see Appendix A).

  1. The NEON Bioarchive shall be:

  1. Designed for efficiency and utility – incorporate system engineering principles

  2. Responsive to needs of external researchers, including the ecological and collections communities

  3. Discoverable with meta-data access; planned to be an extension of NEON’s existing API allowing searches, e.g., based on geolocations. (A central Fulcrum App is being developed for sample management and shipping.)

  4. Capable of efficient and timely sample processing – e.g., accessioned within one month of receipt

  1. The NEON Bioarchive shall:

  1. Curate samples in conformance with accepted best practices, such as those being compiled by the Society for the Preservation of Natural History Collections (SPNHC) -- https://spnhc.biowikifarm.net/wiki

  2. Store samples in perpetuity – at least a 30-year time horizon

  3. Maintain emergency and disaster plans to mitigate risks to the bioarchive

  4. Make samples readily available for loan in a timely manner (i.e., 90% within 3 months after received)

  5. Accommodate destructive and non-destructive uses. Note that destructive uses, which are expected and encouraged for meritorious scientific purposes, should be taken into account when estimating space requirements for the bioarchive over the long term.

  6. Reserve a portion of individual samples for non-destructive uses

NEON samples may be held separately from the repository’s general collections, or they may be incorporated into general collections depending upon which is deemed by mutual agreement to be most cost effective and efficient in making material available to the scientific community.

2.3Technical and Operating Requirements


Collectively, the bioarchive shall have the ability to curate all NEON samples in accordance with the sample specific requirements listed in Appendix A. Specific operating requirements follow below. These may be subject to further discussions with the participating institutions to ensure cost effective and efficient operations and to enhance the observatory’s impact on ecology at the continental scale. Specific terms and conditions will be mutually agreed upon by the NEON Project and participating institutions.

  1. Accessioning: Ninety (90) percent of samples received shall be accessioned within 10 business days of receipt. Ownership of samples shall transfer to the bioarchive upon accessioning subject to clearly articulated and mutually agreed upon rights, roles and responsibilities.

  2. Sorting and Identification: Where practical, specimens will have been be sorted by taxonomic group, preferably at the rank of taxonomic Order or below, prior to delivery to the bioarchive. Prepared specimens will have been labelled. All preserved material will have been prepared in accordance with best practice applicable to the taxon/material being preserved.

  3. Archives: Labeled samples shall be received, preserved, archived and curated by the bioarchive institution(s) following standard/best practices. NEON will transfer ownership of samples to the archive facility – except in cases where prohibited by land owners (e.g., National Park Service). This information will be communicated to the selected institution(s) by NEON as these samples are generated.

  4. Unique Identifiers: NEON requires that all NEON-collected samples contain a NEON unique identifier, which will be attached to the sample and communicated to the bioarchive at the time the new sample is received. Institutional identifiers (preferably globally unique identifiers [GUID]) are also highly encouraged in addition to the required NEON identifier. NEON will need to receive any such institution identifiers as it intends to track all of these identifiers as part of the sample metadata.

  5. Cataloguing: Cataloguing is expected to follow the best standards and practices and as mutually agreed upon with the NEON Project. It may not be necessary to hold all NEON collections separately from the repository’s general collection; but they do need to be catalogued such that they can be easily identified and retrieved as NEON samples.

  6. Loans: NEON-generated samples shall be made available for use by and loan to NEON and external investigators within a reasonable period of time of delivery of samples and metadata by NEON to the bioarchive – 90% of loan requests should be fulfilled within 2-4 weeks. Loan and use of NEON samples shall be in accordance with NEON’s Sample Use Policy (RD [03]) and with the collections community’s standard policies and procedures unless otherwise mutually agreed upon. Each loan may be assigned a DOI by the Bioarchive to facilitate tracking use of samples. A GUID might suffice if the ID is meant for machine (software) consumption. One might also want a human readable Loan ID, which could just be an integer if one is needed for referencing loans in correspondence like overdue letters, etc.

  7. Destructive Sampling: The repository shall formulate destructive sampling policies in consultation with the NEON Project. Consultation with NEON is expected when a proposed research use requires consumption of >50% of a sample, and where the same NEON samples are requested by more than one researcher at a given time. These types of requests will require consultation with NEON before being processed. The NEON Bioarchive shall encourage research use while maintaining a critical set of samples for a “forever archive,” defined as appropriate for each sample type

  8. Deaccession: All deaccession or permanent transfer of samples of NEON generated samples must be coordinated with NEON and approved in writing.

  9. Sample Data Availability: Sample metadata provided by NEON may be made available on the bioarchive web site(s). In addition, NEON will coordinate with the bioarchive to provide data to external data aggregators (e.g., GBIF) as appropriate.

  10. Permitting: NEON will provide copies of all collecting and salvage permits relating to the samples to be transferred to the bioarchive, including incidental vertebrate and invertebrate by-catch mortalities, as needed. Some NEON collection permits (current or future) may specify where certain taxa (e.g., rare species) will be deposited. In the event that a sample needs to be transferred to another institution, NEON will inform the bioarchive and agrees to coordinate these activities and incur the costs associated with this transfer.

  11. Reporting: The NEON Bioarchive shall submit an annual report that summarizes use and disposition of NEON samples. It shall also include any updates to data that result from study of the collections, such as revisions or corrections to sample identifications. The bioarchive shall maintain careful records of the samples available and their use. NEON will work with the Bioarchive to implement means to assess and track scientific impact of the bioarchive.

  12. Timing of Samples: Samples will be shipped from NEON’s Domain Support Facilities, Headquarters or intermediate analytical facilities to the bioarchive facility at varying times throughout the year. An estimate of the numbers of samples to be collected and delivered to the bioarchive each year is presented in Appendix A.

  13. Emergency Plan: The NEON Bioarchive is required to prepare and, execute if needed, an emergency plan to safeguard the integrity of the samples in case of severe weather or other natural disasters, fire, floods, etc.

  14. Agreements: Agreements are expected to be of long-duration (up to 30 years), but may be subject to periodic reviews. Agreements will state terms and conditions related to potential commercial applications.

2.4Information Management


The NEON Bioarchive shall implement a data management system, subject to NEON approval, that is consistent across the bioarchive – whether a single institution or a consortium of several facilities. Commercial-off-the-shelf systems (COTS) are available, such as Specify, Artos, Symbiota, etc. Adoption of a single database is necessary to ensure efficiency and quality control, and to provide a clear audit trail. Use of multiple systems will greatly increase costs and information management complexity.

The NEON Bioarchive is expected to partner with other bioinformatics databases to increase the user awareness of the samples and data available. Use of existing standards and schema will facilitate the use of data across sites and within sites, and with non-NEON data sets. For example, the bioarchive shall take advantage of existing standards such as those maintained by the Taxonomic Databases Working Group (TDWG), which is the standards-setting arm of the Global Biodiversity Information Facility (GBIF).

Cataloging and data basing shall follow best practices of the collections community and as mutually agreed upon by NEON and the bioarchive. Our intent is to use a database schema that incorporates data concepts already established and use by the collections and specific scientific communities. An interface with a sample management system (chain of custody) to ensure a documented lineage from, e.g., whole organisms, tissues, and DNA extracts.

2.5Data Products


NEON will make sample metadata available via the NEON Data Portal such as sample type, species name and sex, NEON unique identifiers, identifiers assigned to samples by the bioarchive or intermediate analytical labs, locality information, collection dates, and other information to be agreed upon. These metadata will be discoverable through the portal and will link samples to their respective observational and measurement data.

2.6Roles and Responsibilities


Collections and Laboratory Analysis Team (CLA): The NEON Bioarchive is supported by CLA, a core group of science and technology staff members with expertise and experience in program management (i.e., preparation, management and monitoring of contract scopes [e.g., statements of work]) and coordination with private and public procurement and acquisition services). This team carries out varied operational tasks, which includes, but is not limited to, communications, and coordination of sample inventory and shipping.

The CLA team plays the key role in bringing together several key elements of the organization to ensure success of this complex and important Observatory activity.



  • Science Operations: Subject matter experts prepare science-based technical specifications, and they assist in evaluating requests for destructive use or consumption of >50% of a given sample

  • Field Operations: Domain field staff are responsible for collecting, processing and shipping of samples. In some cases samples are first sent to a laboratory facility for analysis prior to being shipped to the archive.

  • Data Services: Maintains observatory sample chain of custody system functionality – i.e., until the sample is deposited in the bioarchive. Information on the disposition of samples will be accessible via the data portal. However, once accessioned into the bioarchive, samples will be tracked and reported on by the bioarchive.

  • Calibration and Validation Laboratory: Review annual quality assurance (QA) and quality control (QC) reports provided by the bioarchive.

  • Procurement: prepare agreements in accordance with all applicable laws and federal acquisition regulation.

NEON Bioarchive Advisory Group: An external advisory group will be established to provide input, recommendations, audits, and periodic review of the NEON Bioarchive. Periodic reviews will be conducted periodically to evaluate how well the bioarchive is meeting its goals. The group will also assist in addressing areas of conflict such as competing and large requests.

Users of the NEON Bioarchive are:

  • Responsible for requesting and appropriately managing samples from the Bioarchive, including complying with terms of any award or grant funding research or other use of the samples and with applicable laws and regulations, and return of the samples to the bioarchive if the samples were provided as a loan (as opposed to destructive use or a gift to be archived in another permanent repository such as a museum collection).

  • Responsible for reporting use of samples and data to the bioarchive and/or directly to NEON including use in scientific reports, publications, theses, dissertations, and classroom or other educational use. The DOI attached to each loan or gift of samples or data from the Bioarchive must be used when reporting data use.

2.7Risks and Issues to be Addressed


  • A single standalone archive may pose a higher risk than a distributed network due to having all archived material in one geographic location and lacking back-up facilities to handle sample overflows.

  • Individual collection facilities may be reluctant to accept large amounts of bulk samples that are seen as potentially less valuable to the collections community. Some, such as bulk soil samples, are nontraditional for most collection-holding institutions – though of considerable interest to ecologists.

  • Individual facilities may become reluctant to accept duplicate material over a long period of time. While replicate samples are expected to be of value to the ecological community, sample duplications may be seen as less valuable for reference collections.

  • Individual facilities may be unable to make samples available in a timely manner due to the quantity of material delivered.

  • Individual facilities may propose to house samples for which they have limited experience.

2.8Quality Assurance and Quality Control


Institutions will be qualified on the basis of available documentation and certifications along with site visits. Examples of the types of documents that should be made available include the following:

  1. Plans, Policies and Procedures

    1. Collections Emergency Response and Recovery Plan

    2. Emergency Operations Plan

    3. Integrated Pest Management Plan

    4. Security plan

    5. Long-range Conservation Plan

    6. Data Management Plan and Backup Policy

    7. Collections Management Policy

    8. Destructive Sampling Policy

    9. Accession and Deaccession Policies and Procedures

    10. Collection Procedural Manuals

    11. Loan Agreements and Conditions

  1. Institutional Permits (USFWS, USDA APHIS, CITES)

  2. Database Documentation Standards

  3. Facility Report

  4. Website and evidence of participation in VertNet, iDigBio, and GBIF

  5. Loans and accession files and databases

Annual QA/QC reports shall be furnished by the bioarchive based on criteria mutually agreed upon by the participating institutions and the NEON Project. A NEON Bioarchive Advisory Group will conduct periodic reviews to evaluate how well the bioarchive is meeting its goals.
APPENDIX . Estimated number of NEON samples and specimens

Terrestrial Samples

Pre-2017

2017

Annually thereafter

Storage Condition

Storage Container

Disease--Mosquito pools

0

6,000

20,962

Ultralow

96-well plate*

Disease--Tick pools

5,022

4,230

4,418

Ultralow

96-well plate*

DNA Extractions--Beetle

0

0

4,512

Ultralow

96-well plate*

DNA Extraction-Smammals

0

0

1,920

Ultralow

96-well plate*

DNA Extractions--Mosquito

0

0

1,920

Ultralow

96-well plate*

DNA extractions--Soil

0

0

4,512

Ultralow

96-well plate*

Ground beetle by-catch in bulk

9,956

5,012

3,901

95% ETOH

50mL Falcon tubes

Ground beetle pinned/pointed

0

0

9400

dry

Unit trays

Ground beetle pooled

1,396

1,063

2,444

95% ETOH

50mL Falcon tubes

Leaf litter

90

120

120

dry

20mL vial

Mosquitoes pinned/pointed

4,006

6,080

3,196

dry

Unit trays

Mosquitos Bulk

1,569

2,050

3,478

Ultralow

2-15 mL vials

Plant (biomass)

204

272

400

dry

20mL vial

Plant belowground (biomass)

2,977

460

320

Ultralow

20mL vial

Plant voucher specimens

390

640

940

dry

Individual mounts

Small mammal blood

0

0

2,820

Ultralow

2 mL cryovial

Small mammal ear punch

0

0

3,525

Ultralow

2 mL cryovial

Small mammal fecal sample

0

0

5,076

Ultralow

2 mL cryovial

Small mammal hairs/whiskers

0

0

3,525

dry

Archival coin envelope

Small mammal specimens

0

0

940

Dry or 70% ETOH

Individual or lots

Soil

6,485

8,840

12,220

Ultralow

1490 in 50mL conical tubes; remainder in 2oz. Whirlpaks

Soil (every 5-10 yrs) Air dried

776

271

360

dry

250mL jar

Ticks

0

0

2961

95% ETOH

2mL vial

Subtotal


32,871

37,055


93,870

 

 

*Number of well-plates = (sample number) ÷ 96

Tower Samples

Pre-2017

2017

#/Year

Storage Condition

Storage Container

Wet Deposition

0

0

1,118

-4°C

0.5-1L jar

Dry Deposition

0

0

156

dry

Filter (8"x10")

 Subtotal

0

0

1,274




 




Aquatic Samples

Pre-2017

2017

Annually Thereafter

Storage Condition

Storage Container

Algae: Periphyton, seston, phytoplankton – diatoms

0

783

918

Freeze dried

Vials

Algae: Periphyton, seston, phytoplankton – diatoms

0

783

918

dry

Glass slides

Algae: Periphyton, seston, phytoplankton – soft algae

0

783

918

glutaraldehyde

60 mL jar or smaller

Macroalgae

0

435

510

glutaraldehyde

60mL jar

Aquatic macrophyte vouchers

52

435

510

dry

Herbarium paper

Aquatic mosses/lichens/ liverworts

52

435

510

dry

Herbarium packet

Macroinvertebrate specimens

267

696

816

70% ETOH +5% glycerol

500mL jar or smaller

Zooplankton specimens

49

72

63

70% ETOH +5% glycerol

500mL jar or smaller

Fish voucher specimens

0

250

1,020

70% ETOH

Individual/lot

Fish tissue

0

0

1,700

95% ETOH

2-10mL vial

Macroinvertebrate homogenates

0

0

306

Ultralow or 95% ETOH

2mL cryovial

Zooplankton homogenates

0

0

63

Ultralow or 95% ETOH

2mL cryovial

Aquatic Microbes--Benthic

210

342

576

Ultralow

Cryovial or Sterivex filters

Aquatic Microbes--Water

336

522

612

Ultralow

Sterivex filters

 Subtotal

966

5,536

9,440









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