obis

## Dataset Description
- **Repository:** https://huggingface.co/datasets/louisbrulenaudet/obis
- **Leaderboard:** N/A
- **Point of Contact:** [Louis Brulé Naudet](mailto:[e-mail])

<img src="assets/thumbnail.jpg">

# OBIS Marine Species Observation Dataset

More than 20 OBIS (Ocean Biodiversity Information System) nodes around the world connect 500 institutions from 56 countries. Collectively, they have provided over 45 million observations of nearly 120,000 marine species, ranging from bacteria to whales, from the surface to 10,900 meters depth, and from the tropics to the poles. The datasets are integrated, allowing seamless search and mapping by species name, higher taxonomic level, geographic area, depth, time, and environmental parameters. OBIS originates from the Census of Marine Life (2000-2010) and was adopted as a project under IOC-UNESCO’s International Oceanographic Data and Information (IODE) programme in 2009.

## Objectives

1. **Provide a comprehensive scientific knowledge base**: The dataset aims to be the world’s largest repository on the diversity, distribution, and abundance of all marine organisms, contributing to Aichi biodiversity target 19.
2. **Facilitate biogeographic and environmental data integration**: This integration aids climate change studies by combining biogeographic information with physical and chemical environmental data.
3. **Support global marine biodiversity monitoring**: The dataset contributes to a global approach through guidelines on standards and best practices, including Essential Ocean Variables, observing plans, and indicators in collaboration with other IOC programs.
4. **Inform policy making**: By supporting assessments of the state of marine biological diversity, the dataset helps inform policy makers and responds to needs of regional and global processes such as the UN World Ocean Assessment (WOA) and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES).
5. **Support marine spatial planning**: The data assists in identifying biologically important marine and coastal habitats for the development of marine spatial plans and other area-based management plans, such as Ecologically or Biologically Significant marine Areas (EBSAs) under the Convention on Biological Diversity.
6. **Enhance institutional and professional capacity**: As part of IOC’s Ocean Teacher Global Academy (OTGA), the dataset contributes to capacity building in marine biodiversity and ecosystem data collection, management, analysis, and reporting.
7. **Provide educational and research support**: The dataset offers guidance on using biodiversity data for education and research, providing state-of-the-art services to society, including decision-makers.
8. **Foster international collaboration**: The dataset serves as a global platform for collaboration between national and regional marine biodiversity and ecosystem monitoring programs, enhancing contributions to the Global Ocean Observing System (GOOS) and the Global Earth Observing System of Systems (GEOSS).

## Dataset Fields

| Field | Remarks |
|--------------------------------|------------------------------------------------------------------------------------------------------------------------------|
| id | Globally unique identifier assigned by OBIS. |
| dataset_id | Internal dataset identifier assigned by OBIS. |
| decimalLongitude | Parsed and validated by OBIS. |
| decimalLatitude | Parsed and validated by OBIS. |
| date_start | Unix timestamp based on eventDate (start). |
| date_mid | Unix timestamp based on eventDate (middle). |
| date_end | Unix timestamp based on eventDate (end). |
| date_year | Year based on eventDate. |
| scientificName | Valid scientific name based on the scientificNameID or derived by matching the provided scientificName with WoRMS. |
| originalScientificName | The scientificName as provided. |
| minimumDepthInMeters | Parsed and validated by OBIS. |
| maximumDepthInMeters | Parsed and validated by OBIS. |
| coordinateUncertaintyInMeters | Parsed and validated by OBIS. |
| flags | Quality flags added by OBIS. The quality flags are documented here. |
| dropped | Record dropped by OBIS quality control? |
| absence | Absence record? |
| shoredistance | Distance from shore in meters added by OBIS quality control, based on OpenStreetMap. Negative value indicates that the observation was inland by -1 times that distance. |
| bathymetry | Bathymetry added by OBIS. Bathymetry values based on EMODnet Bathymetry and GEBCO, see [Data references](https://github.com/iobis/xylookup). |
| sst | Sea surface temperature added by OBIS. sst values based on Bio-Oracle, see [Data references](https://github.com/iobis/xylookup). |
| sss | Sea surface salinity added by OBIS. sss values based on Bio-Oracle, see [Data references](https://github.com/iobis/xylookup). |
| marine | Marine environment flag based on WoRMS. |
| brackish | Brackish environment flag based on WoRMS. |
| freshwater | Freshwater environment flag based on WoRMS. |
| terrestrial | Terrestrial environment flag based on WoRMS. |
| taxonRank | Based on WoRMS. |
| AphiaID | AphiaID for the valid name based on the scientificNameID or derived by matching the provided scientificName with WoRMS. |
| redlist_category | IUCN Red List category. |
| superdomain | Based on WoRMS. |
| domain | Based on WoRMS. |
| kingdom | Based on WoRMS. |
| subkingdom | Based on WoRMS. |
| infrakingdom | Based on WoRMS. |
| phylum | Based on WoRMS. |
| phylum (division) | Based on WoRMS. |
| subphylum (subdivision) | Based on WoRMS. |
| subphylum | Based on WoRMS. |
| infraphylum | Based on WoRMS. |
| parvphylum | Based on WoRMS. |
| gigaclass | Based on WoRMS. |
| megaclass | Based on WoRMS. |
| superclass | Based on WoRMS. |
| class | Based on WoRMS. |
| subclass | Based on WoRMS. |
| infraclass | Based on WoRMS. |
| subterclass | Based on WoRMS. |
| superorder | Based on WoRMS. |
| order | Based on WoRMS. |
| suborder | Based on WoRMS. |
| infraorder | Based on WoRMS. |
| parvorder | Based on WoRMS. |
| superfamily | Based on WoRMS. |
| family | Based on WoRMS. |
| subfamily | Based on WoRMS. |
| supertribe | Based on WoRMS. |
| tribe | Based on WoRMS. |
| subtribe | Based on WoRMS. |
| genus | Based on WoRMS. |
| subgenus | Based on WoRMS. |
| section | Based on WoRMS. |
| subsection | Based on WoRMS. |
| series | Based on WoRMS. |
| species | Based on WoRMS. |
| subspecies | Based on WoRMS. |
| natio | Based on WoRMS. |
| variety | Based on WoRMS. |
| subvariety | Based on WoRMS. |
| forma | Based on WoRMS. |
| subforma | Based on WoRMS. |

## Source

OBIS (YEAR) Ocean Biodiversity Information System. Intergovernmental Oceanographic Commission of UNESCO. [https://obis.org](https://obis.org).

## Citing & Authors

If you use this dataset in your research, please use the following BibTeX entry.

```BibTeX
@misc{HFforLegal2024,
author = {Louis Brulé Naudet},
title = {OBIS Marine Species Observation Dataset},
year = {2024}
howpublished = {\url{https://huggingface.co/datasets/louisbrulenaudet/obis}},
}
```

## Feedback

If you have any feedback, please reach out at [[e-mail]](mailto:[e-mail]).

## 数据集描述
- **仓库地址**：https://huggingface.co/datasets/louisbrulenaudet/obis
- **排行榜**：无（N/A）
- **联系人**：[Louis Brulé Naudet](mailto:[e-mail])

<img src="assets/thumbnail.jpg">

# OBIS海洋物种观测数据集

全球超过20个OBIS（海洋生物多样性信息系统，Ocean Biodiversity Information System）节点连接了来自56个国家的500家机构，累计提供了近12万种海洋生物的超4500万条观测记录，涵盖从细菌到鲸鱼的各类生物、从海面至10900米深度的海域以及从热带到极地的所有区域。该数据集已完成整合，支持通过物种名称、高级分类阶元、地理区域、深度、时间及环境参数实现无缝检索与制图。OBIS起源于“海洋生物普查（2000-2010年）”，并于2009年被纳入联合国教科文组织政府间海洋学委员会（IOC-UNESCO）的国际海洋学数据与信息（IODE）计划项目。

## 数据集目标

1. **构建全面的科学知识库**：本数据集旨在成为全球规模最大的涵盖所有海洋生物多样性、分布与丰度的资源库，助力实现《爱知生物多样性目标》第19项。
2. **促进生物地理与环境数据整合**：通过将生物地理信息与物理、化学环境数据相结合，该数据集可为气候变化研究提供支撑。
3. **支持全球海洋生物多样性监测**：本数据集通过与其他IOC计划合作制定标准与最佳实践指南（包括关键海洋变量、观测计划及指标），助力构建全球海洋生物多样性监测体系。
4. **为政策制定提供依据**：通过支撑海洋生物多样性现状评估，该数据集可为政策制定者提供决策参考，并响应联合国世界海洋评估（WOA）及生物多样性和生态系统服务政府间科学政策平台（IPBES）等全球与区域进程的需求。
5. **支持海洋空间规划**：该数据集可协助识别具有重要生物意义的海洋与沿岸栖息地，用于制定海洋空间规划及其他基于区域的管理计划，例如《生物多样性公约》框架下的“生态或生物重要海洋区域（EBSAs）”。
6. **提升机构与专业能力**：作为IOC“海洋教师全球学院（OTGA）”的组成部分，本数据集助力提升海洋生物多样性与生态系统数据收集、管理、分析及报告相关的能力建设水平。
7. **提供教育与研究支持**：本数据集为教育与研究场景中生物多样性数据的使用提供指导，为包括决策者在内的社会各界提供前沿服务。
8. **推动国际合作**：本数据集作为国家与区域海洋生物多样性及生态系统监测计划间开展合作的全球平台，助力提升对全球海洋观测系统（GOOS）及全球地球观测系统系统（GEOSS）的贡献。

## 数据集字段

| 字段名称 | 备注说明 |
|--------------------------------|------------------------------------------------------------------------------------------------------------------------------|
| id | 由OBIS分配的全局唯一标识符。 |
| dataset_id | 由OBIS分配的内部数据集标识符。 |
| decimalLongitude | 经OBIS解析与验证的十进制经度。 |
| decimalLatitude | 经OBIS解析与验证的十进制纬度。 |
| date_start | 基于eventDate（起始时间）生成的Unix时间戳。 |
| date_mid | 基于eventDate（中间时间）生成的Unix时间戳。 |
| date_end | 基于eventDate（结束时间）生成的Unix时间戳。 |
| date_year | 基于eventDate提取的年份。 |
| scientificName | 基于scientificNameID验证的科学名称，或通过将提供的科学名称与WoRMS（世界海洋物种登记册，World Register of Marine Species）匹配得到的有效科学名称。 |
| originalScientificName | 原始提供的科学名称。 |
| minimumDepthInMeters | 经OBIS解析与验证的最小深度（单位：米）。 |
| maximumDepthInMeters | 经OBIS解析与验证的最大深度（单位：米）。 |
| coordinateUncertaintyInMeters | 经OBIS解析与验证的坐标不确定性（单位：米）。 |
| flags | OBIS添加的质量标记。相关质量标记说明可参见[此处](https://github.com/iobis/xylookup)。 |
| dropped | 是否为OBIS质量控制流程中被剔除的记录？ |
| absence | 是否为物种存在缺失记录？ |
| shoredistance | OBIS质量控制流程中基于OpenStreetMap添加的距岸距离（单位：米）。负值表示观测点位于内陆，其绝对值为距岸距离的相反数。 |
| bathymetry | OBIS添加的水深数据。水深数据基于EMODnet Bathymetry和GEBCO，详见[数据引用](https://github.com/iobis/xylookup)。 |
| sst | OBIS添加的海表温度数据。sst数据基于Bio-Oracle，详见[数据引用](https://github.com/iobis/xylookup)。 |
| sss | OBIS添加的海表盐度数据。sss数据基于Bio-Oracle，详见[数据引用](https://github.com/iobis/xylookup)。 |
| marine | 基于WoRMS生成的海洋环境标记。 |
| brackish | 基于WoRMS生成的半咸水环境标记。 |
| freshwater | 基于WoRMS生成的淡水环境标记。 |
| terrestrial | 基于WoRMS生成的陆地环境标记。 |
| taxonRank | 基于WoRMS生成的分类阶元。 |
| AphiaID | 基于scientificNameID生成的有效名称对应的AphiaID，或通过将提供的科学名称与WoRMS匹配得到的AphiaID。 |
| redlist_category | IUCN红色名录等级。 |
| superdomain | 基于WoRMS生成的总域。 |
| domain | 基于WoRMS生成的域。 |
| kingdom | 基于WoRMS生成的界。 |
| subkingdom | 基于WoRMS生成的亚界。 |
| infrakingdom | 基于WoRMS生成的下总界。 |
| phylum | 基于WoRMS生成的门。 |
| phylum (division) | 基于WoRMS生成的门（亦称为division，仅适用于部分类群）。 |
| subphylum (subdivision) | 基于WoRMS生成的亚门（亦称为subdivision，仅适用于部分类群）。 |
| subphylum | 基于WoRMS生成的亚门。 |
| infraphylum | 基于WoRMS生成的下门。 |
| parvphylum | 基于WoRMS生成的小门。 |
| gigaclass | 基于WoRMS生成的超巨纲。 |
| megaclass | 基于WoRMS生成的巨纲。 |
| superclass | 基于WoRMS生成的总纲。 |
| class | 基于WoRMS生成的纲。 |
| subclass | 基于WoRMS生成的亚纲。 |
| infraclass | 基于WoRMS生成的下纲。 |
| subterclass | 基于WoRMS生成的次纲。 |
| superorder | 基于WoRMS生成的总目。 |
| order | 基于WoRMS生成的目。 |
| suborder | 基于WoRMS生成的亚目。 |
| infraorder | 基于WoRMS生成的下目。 |
| parvorder | 基于WoRMS生成的小目。 |
| superfamily | 基于WoRMS生成的总科。 |
| family | 基于WoRMS生成的科。 |
| subfamily | 基于WoRMS生成的亚科。 |
| supertribe | 基于WoRMS生成的总族。 |
| tribe | 基于WoRMS生成的族。 |
| subtribe | 基于WoRMS生成的亚族。 |
| genus | 基于WoRMS生成的属。 |
| subgenus | 基于WoRMS生成的亚属。 |
| section | 基于WoRMS生成的组。 |
| subsection | 基于WoRMS生成的亚组。 |
| series | 基于WoRMS生成的系。 |
| species | 基于WoRMS生成的种。 |
| subspecies | 基于WoRMS生成的亚种。 |
| natio | 基于WoRMS生成的群（natio，仅适用于部分类群）。 |
| variety | 基于WoRMS生成的变种。 |
| subvariety | 基于WoRMS生成的亚变种。 |
| forma | 基于WoRMS生成的变型。 |
| subforma | 基于WoRMS生成的亚变型。 |

## 数据来源

OBIS（年份）《海洋生物多样性信息系统》。联合国教科文组织政府间海洋学委员会。[https://obis.org](https://obis.org)。

## 引用与作者

若您在研究中使用本数据集，请使用以下BibTeX引用条目。

BibTeX
@misc{HFforLegal2024,
author = {Louis Brulé Naudet},
title = {OBIS海洋物种观测数据集},
year = {2024}
howpublished = {url{https://huggingface.co/datasets/louisbrulenaudet/obis}},
}

## 反馈

如有任何反馈，请联系[Louis Brulé Naudet](mailto:[e-mail])。