小型數(shù)據(jù)庫

If you’re a scientist, especially one performing a lot of your research alone, you probably have more than one spreadsheet of important data that you just haven’t gotten around to writing up yet. Maybe you never will. Sitting idle on a hard drive, that “dark data” could prove very useful to someone in the future (or even someone in the present), especially as our climate and society changes.

如果您是一名科學(xué)家，尤其是一個(gè)人獨(dú)自進(jìn)行大量研究，那么您可能擁有多個(gè)重要數(shù)據(jù)電子表格，而這些電子數(shù)據(jù)您還沒有寫出來。 也許你永遠(yuǎn)不會(huì)。 閑置在硬盤上的“黑暗數(shù)據(jù)”可能對(duì)將來的某人(甚至現(xiàn)在的某人)非常有用，尤其是在我們的氣候和社會(huì)變化的情況下。

What are you going to do with those files? How are you going to preserve them?

您將如何處理這些文件？ 您將如何保存它們？

If you’re like me, maybe you’ve felt the terror of losing data every time you moved your files to a new computer or moved your research to a new job. Did you remember to back up that spreadsheet from your brilliant pet project from 7 years ago? If you did back it up, are you sure you backed up the most recent version? It’s sobering to imagine other people have gone through this and lost potentially valuable species records, survey data, and field observations.

如果您像我一樣，也許您每次將文件移至新計(jì)算機(jī)或?qū)⒀芯恳浦列鹿ぷ鲿r(shí)都會(huì)感到丟失數(shù)據(jù)的恐懼。 您是否還記得從7年前的出色寵物項(xiàng)目中備份了該電子表格？ 如果您備份過，是否確定備份了最新版本？ 想象其他人經(jīng)歷了這一過程并失去了可能有價(jià)值的物種記錄，調(diào)查數(shù)據(jù)和實(shí)地觀察結(jié)果，這真是令人震驚。

營救的數(shù)字?jǐn)?shù)據(jù)存儲(chǔ)庫 (Digital Data Repositories to the Rescue)

In the years before I returned to graduate school, I worked for a science nonprofit on Nantucket Island, Massachusetts, and this problem haunted me all the time. Over nearly a decade there, I accumulated spreadsheets filled with very localized, ecological data, but had no way to organize it, save it, and share it. Fortunately, a solution is emerging in the form of digital repositories backed with robust metadata schemes and indexing services. Importantly, some of these repositories are accessible to everyone, and no university affiliation is required.

回到研究生院的前幾年，我在馬薩諸塞州楠塔基特島的一家科學(xué)非營利組織工作，這個(gè)問題一直困擾著我。 在那附近的近十年中，我積累了電子表格，其中包含非常本地化的生態(tài)數(shù)據(jù)，但是卻無法組織，保存和共享它。 幸運(yùn)的是，以強(qiáng)大的元數(shù)據(jù)方案和索引服務(wù)為后盾的數(shù)字存儲(chǔ)庫的形式正在出現(xiàn)一種解決方案。 重要的是，每個(gè)人都可以訪問其中一些存儲(chǔ)庫，并且不需要大學(xué)附屬機(jī)構(gòu)。

In May 2020, Meghan Mitchell, Christopher Tillman Neal and I launched a digital repository for the Nantucket Biodiversity Initiative (NBI). The repository stores and protects environmental and ecology research data from around Nantucket, but it is focused on projects funded by NBI. Visit the Nantucket Biodiversity Digital Repository and browse through the files to learn about bat counts, spider surveys, sandplain grassland research, and much more.

2020年5月，我和梅根·米切爾 ( Meghan Mitchell) ， 克里斯托弗·蒂爾曼·尼爾 ( Christopher Tillman Neal)共同為楠塔基特生物多樣性倡議 (NBI)建立了一個(gè)數(shù)字倉庫。 該存儲(chǔ)庫可以存儲(chǔ)和保護(hù)Nantucket周圍的環(huán)境和生態(tài)研究數(shù)據(jù)，但它的重點(diǎn)是由NBI資助的項(xiàng)目。 訪問Nantucket生物多樣性數(shù)字資料庫 ，瀏覽文件，以了解蝙蝠數(shù)量，蜘蛛調(diào)查，灘涂草地研究等更多信息。

A snapping turtle on Nantucket. Over half of Nantucket Island is conservation land and scientific species inventories date back to the late 1800’s. There is a wealth of information that would benefit from being published to a repository. Photo: Andrew Mckenna-Foster楠塔基特島上的一只鱷龜。 楠塔基特島一半以上的土地是自然保護(hù)區(qū)，科學(xué)物種清單可追溯到1800年代后期。 通過發(fā)布到存儲(chǔ)庫中可以獲得大量信息。 照片：安德魯·麥肯納·福斯特(Andrew Mckenna-Foster)

We used Zenodo, a free platform that allows anyone to upload research related files. Zenodo stores the files forever, makes them searchable on the internet, and even gives them a digital object identifier (DOI). However, uploading your files to a repository is the easy part of the solution; to make data useful far into the future, it is crucial to follow the core principles of data publishing and sharing. Uploading data with no context makes it one more piece of junk in the vastness of the internet.

我們使用了Zenodo ，這是一個(gè)免費(fèi)平臺(tái)，任何人都可以上傳與研究相關(guān)的文件。 Zenodo永久存儲(chǔ)文件，使它們可以在Internet上搜索，甚至為它們提供數(shù)字對(duì)象標(biāo)識(shí)符(DOI)。 但是，將文件上傳到存儲(chǔ)庫是該解決方案的簡單部分。 為了使數(shù)據(jù)對(duì)將來有用，遵循數(shù)據(jù)發(fā)布和共享的核心原則至關(guān)重要。 在沒有上下文的情況下上傳數(shù)據(jù)會(huì)使它在互聯(lián)網(wǎng)的廣闊空間中變得更加垃圾。

記錄數(shù)據(jù)很困難，但是絕對(duì)必要 (Documenting Data is Difficult but Absolutely Essential)

Published data should be FAIR: Findable, Accessible, Interoperable, and Reusable. In practice, this means

發(fā)布的數(shù)據(jù)應(yīng)公平 ：可查找，可訪問，可互操作和可重用。 實(shí)際上，這意味著

• Describing the data with a solid description, useful keywords, and author information (metadata)
  用可靠的描述，有用的關(guān)鍵字和作者信息(元數(shù)據(jù))描述數(shù)據(jù)
• Using a standard metadata scheme so that the information can be easily shared
  使用標(biāo)準(zhǔn)的元數(shù)據(jù)方案，以便可以輕松共享信息
• Uploading the files in an open format (like CSV)
  以開放格式(例如CSV)上傳文件
• Licensing the data so that people and machines will understand how the data can be used.
  授予數(shù)據(jù)許可，以便人和機(jī)器可以理解如何使用數(shù)據(jù)。

That is only the bare minimum. While Zenodo and other free repository platforms like figshare and Dataverse simplify this process, it still requires work and planning.

那只是最低限度。 雖然Zenodo和其他免費(fèi)的存儲(chǔ)庫平臺(tái)(例如figshare和Dataverse)簡化了此過程，但仍需要進(jìn)行工作和計(jì)劃??。

The meat of our project was working with NBI to create a workflow that curates and applies metadata to all reports and datasets before publication. If you want to set up a repository for yourself or your organization, this is where you should focus most of your energy. We built a documentation site on GitHub that describes the process in detail and is free to copy.

我們項(xiàng)目的重點(diǎn)是與NBI合作創(chuàng)建一個(gè)工作流，該工作流在發(fā)布之前對(duì)所有報(bào)表和數(shù)據(jù)集進(jìn)行策展并將其應(yīng)用于元數(shù)據(jù)。 如果您想為自己或您的組織建立存儲(chǔ)庫，則應(yīng)在此處集中精力。 我們在GitHub上建立了一個(gè)文檔站點(diǎn) ，該站點(diǎn)詳細(xì)描述了該過程，可以免費(fèi)復(fù)制。

那么，結(jié)果是什么？ (So, What are the Outcomes?)

The repository is growing as we curate and upload reports and data going back to 2005. More importantly,

隨著我們整理和上載可追溯到2005年的報(bào)告和數(shù)據(jù)，該信息庫正在增長。更重要的是，

• NBI now has a permanent, accessible, and shareable library of the research it has supported.
  NBI現(xiàn)在擁有其支持的研究的永久，可訪問且可共享的庫。
• Researchers who work on or near Nantucket now have a way to publish their data and reports.
  現(xiàn)在，在Nantucket上或附近工作的研究人員可以發(fā)布其數(shù)據(jù)和報(bào)告。
• People looking for data and information for the area can now browse current and past research. Importantly, they can cite any information they use, giving authors the credit they deserve.
  正在尋找該地區(qū)數(shù)據(jù)和信息的人們現(xiàn)在可以瀏覽當(dāng)前和過去的研究。 重要的是，他們可以引用自己使用的任何信息，從而為作者提供應(yīng)有的信譽(yù)。
• I can sleep at night knowing the data I spent years collecting has a permanent home.
  我知道自己花了數(shù)年收集的數(shù)據(jù)擁有永久性住所，因此我可以在晚上入睡。

A summary of the repository as of August 2020. We use Zenodo’s API to harvest metadata from the Nantucket Biodiversity Digital Repository for visualization using Python. These charts are only possible because the workflow we designed controls how keywords are assigned.截至2020年8月的存儲(chǔ)庫摘要。我們使用Zenodo的API從Nantucket生物多樣性數(shù)字存儲(chǔ)庫中收集元數(shù)據(jù)，以便使用Python進(jìn)行可視化。 這些圖表是唯一可行的，因?yàn)槲覀冊O(shè)計(jì)的工作流程控制著關(guān)鍵字的分配方式。

As NBI continues to support research and add files to this repository, publishing the raw data, not just a project report, will be especially important. With that data in hand, researchers in 10, 50, or 100 years will be able to reproduce and directly compare data from species surveys, population surveys, and management regimes.

隨著NBI繼續(xù)支持研究并向該存儲(chǔ)庫添加文件，發(fā)布原始數(shù)據(jù)(而不僅僅是項(xiàng)目報(bào)告)將變得尤為重要。 有了這些數(shù)據(jù)，研究人員將能夠在10、50或100年內(nèi)重現(xiàn)并直接比較物種調(diào)查，種群調(diào)查和管理制度中的數(shù)據(jù)。

存儲(chǔ)庫已被使用 (The Repository Is Already Being Used)

The icing on the cake is that since the repository became operational, it has already proven useful: I recently shared a dataset on Nantucket tarantulas with another spider researcher who was looking for a way to cite our observations.

錦上添花的是，自該庫投入運(yùn)行以來，它已被證明是有用的：我最近與另一位蜘蛛研究人員共享了Nantucket tarantulas的數(shù)??據(jù)集，該研究人員正在尋找一種方法來引用我們的觀察結(jié)果。

I hope you consider publishing your data whenever possible and choose to follow the FAIR principles. The open science community is growing rapidly and offers numerous resources for anyone to get started. I am always open to questions and collaborations so please contact me if you’re interested in working together.

我希望您考慮在任何可能的時(shí)候發(fā)布數(shù)據(jù)，并選擇遵循FAIR原則。 開放式科學(xué)界正在Swift發(fā)展，并為任何人提供了眾多的資源。 我總是對(duì)問題和合作持開放態(tài)度，因此，如果您有興趣合作，請(qǐng)與我聯(lián)系。

翻譯自: https://medium.com/swlh/if-you-work-in-small-science-are-you-leveraging-data-repositories-357cabfc2326

小型數(shù)據(jù)庫

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