CHPO

来自中国HPO翻译委员会
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Chinese Human Phenotype Ontology Consortium (CHPO)

中文人类表型标准用语联盟

背景

随着基因测序技术的发展,人们获取自身基因组数据的途径越来越便捷,科学研究的重点转向了如何解读这些基因组数据与人类疾病的关系。随着对人类疾病研究的逐渐深入,科学家们越来越意识到临床表型数据的重要性,将基因型与表型数据联合分析,成为众多疾病研究的一个方向。

然而目前在国内,大部分医疗、科研工作者所使用的表型描述词语并没有统一的标准,大多数医院信息系统中记录的临床表型数据都是非结构化的自然语句,这对人类疾病、尤其是遗传性疾病的临床研究和交流带来了不便,对后期的数据分析和挖掘也造成了很大的困扰,因此,在中国建立一套标准的临床表型用语变得非常重要。

HPO(Human Phenotype Ontology,人类表型标准用语,人类表型本体)项目旨在提供一套描述人类疾病所致的异常表型的标准词语集。目前HPO已收录约11000个词条,每个词条对应一种异常表型,HPO对所有的词条进行了系统的分类管理。为方便HPO在临床、科研领域的应用,HPO对OMIM、Orphanet和DECIPHER中记录的7000多种遗传病提供了HPO注释;同时,还为约4000种常见疾病提供了HPO注释。此外,HPO开发组还在持续地进行词条的维护和完善工作。

Background

With the continued development of gene sequencing technology, the focus of scientific research is increasingly switching to how to interpret the relationship between the vast amount of genomic data generated and human diseases. Scientists are increasingly aware of the importance of clinical phenotypic data. Therefore, integrating analysis of genomic data and phenotypic data has become an important direction for disease research. However, at present in China, most phenotypic descriptors used by medical professionals and scientific researchers do not have unified standards. Most of the clinical phenotypic data recorded in hospital information systems are unstructured natural sentences. This poses a challenge to clinical research and communication as well as data analysis and mining, especially for hereditary diseases. It is therefore very important to establish a set of standards for terminology on clinical phenotypes in China.

The Human Phenotype Ontology (HPO) database aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms (still growing) and over 115,000 annotations to hereditary diseases. Each term in the HPO describes a phenotypic abnormality and has systemic annotations. In order to serve clinical and scientific uses, HPO is being developed for over 7,000 hereditary diseases using existing available medical literature, Orphanet, DECIPHER and OMIM. The HPO also provides a large set of HPO annotations to approximately 4,000 common diseases. In addition, HPO creators are continuously working to add new terms and improve the system.

CHPO的成立

在CHPO建立过程中,2015年底,由华大基因团队、美国医学遗传学学院会员张巍教授和南加州大学生物信息学专家王凯教授共同翻译HPO词条,王凯教授搭建了wiki网站;中日友好医院顾卫红教授在相关方协调沟通组织方面付出了很大的努力;北京协和医学院黄尚志教授给予了大力的支持。2016年初,在华大基因杨焕明院士与HPO创始人Peter Robinson教授的推动下,成立了中文人类表型标准用语联盟(The Chinese Human Phenotype Ontology Consortium, CHPO)。

Foundation of CHPO

In 2015, A team from Beijing Genomics Institute (BGI), together with Prof. Zhang Wei (a member of the American Medical Genetics Society) and Prof. Kai Wang ( a bioinformatics expert from the University of Southern California), translated all existing HPO terms in to Chinese. Prof. Kai Wang subsequently established a Wiki website for collaborative editing and improvements. Prof. Weihong Gu from the China-Japan Friendship Hospital paid great efforts with regards to the coordination and communication of relevant parties. Prof. Shangzhi Huang from Peking Union Medical College also contributed greatly. At the beginning of 2016, the Chinese Human Phenotype Ontology Consortium (CHPO) was established under the impetus of Prof. Yang Huanming (one of the founders of BGI) and Prof. Peter Robinson (founder of HPO).

CHPO工作目标

CHPO是一个志愿参与的项目,旨在中国建立一个开放平台, 联合各相关领域专业人士,逐步建立中文临床表型术语标准,并让其指导、服务于中文使用者的临床和科研工作。在此承诺CHPO与临床机构、基础研究机构、专业协会和患者组织无利益冲突,并致力于在2017年前实现两个目标: 1. 提供人类表型的中文标准术语 2. 提供一个高效的中文人类表型搜索引擎

CHPO Aims

CHPO is a volunteer-based project and was set up as an open platform in China to benefit the public. CHPO unites prestigious experts and organizations in order to synergize their efforts, while also ensuring that there is no-conflict of interest against the basic research community and patient organizations. CHPO has two main objectives by the year 2017, namely to deliver a well-organized Chinese ontology and also an efficient search engine for the CHPO platform.

CHPO管理

CHPO由一个指导委员会、两个工作组管理。这些机构的组成和授权如下所述:

CHPO指导委员会及维护组和HPO联络组

指导委员会主席 Peter Robinson教授和杨焕明教授是委员会联席主席,主要职责包括指导委员会的召集和主持决议程序。

欧洲和美国成员:(由Peter Robinson教授提名)

总协调人:顾卫红

中国成员

  • 黄尚志,国内知名遗传学家,曾任北京协和医学院遗传室主任,世界卫生组织遗传病社区控制合作中心主任,中国罕见病发展中心顾问
职责:向中国医学院校宣传推广CHPO
  • 王凯,博士,哥伦比亚大学副教授,生物信息学专家
职责:开发CHPO编辑平台和搜索引擎
  • 顾卫红,博士,临床遗传专家,中日友好医院神经内科运动障碍与神经遗传病研究中心负责人,中国罕见病发展中心顾问
职责:在临床医疗系统宣传推广CHPO
  • 张巍,博士,美国医学遗传学院专家委员,贝勒医学院客座副教授,广州嘉检医学主任,经美国医学遗传学会(ABMG)认证的临床分子遗传学与临床生化遗传学专家
职责:负责招募与教育来自大学和医院的志愿者。
  • 彭智宇,博士,生物信息学专家,华大基因临床研究和产品开发总负责人
职责:将CHPO作为临床报告标准应用于遗传实验室
  • 李宁,博士,国际罕见病研究联盟指导委员会委员,GenomeDenmark指导委员会委员
职责:在中国法律框架内优化伦理和监管流程,保护CHPO版权和品牌免于非授权的商业化,和负责CHPO指导委员会公共关系管理

Wiki网站和搜索引擎设计&维护组:顾卫红、王凯、朱赢、张林、秦建虎、黄辉、张巍

HPO联络组:李宁、王凯、顾卫红、李勇平、张林

CHPO指导委员会的授权

1. 制定CHPO的政策和指导方针 2. 与非营利性基金合作,解决CHPO评定的优先项目,如经由CHPO工作组确认的项目 3. 监督进度,向联席主席报告进展 4. 商定传播策略以确保及时、准确地宣传委员会的目标与工作进展 5. 如果出现任何矛盾,将提供座谈会协助解决 6. 推动加强各工作组之间的沟通 7. 确保与基础研究团体和病人组织无利益冲突

CHPO Governance

CHPO is governed through one Steering Committee and six working groups. The mandate and composition of these bodies are described below.

Compositions of CHPO Steering Committee and the leadership in the six working groups

Co-Chair Prof. Peter Robinson and Prof. Huanming YANG; main responsibilities include the steering committee's convening and presiding process.

Members from Europe and US: (nominated by Prof. Peter Robinson)

General Coordinator: Prof. Weihong GU

Members from China:

1, Shangzhi HUANG, Co-Director of Human Genetics Society of China
Famous geneticist, served as the Beijing Union Medical College genetic room director, director of World Health Organization Center for genetic disease community control cooperation, senior consultant at the Chinese Rare Diseases Research Center
Responsibility: leading the working group to introduce CHPO into Chinese medical schools
2, Kai WANG, Ph.D. Associate Professor in Columbia University, expert in bioinformatics
Responsibility: leading the working group to develop and optimize the wiki website and searching engine for CHPO
3, Weihong GU, M.D., Ph.D. Clinical geneticist
Director of Movement Disorder and Neurogenetics Research Center in China-Japan Friendship Hospital, senior consultant at the Chinese Rare Diseases Research Center
Responsibility: leading the working group to advocate CHPO in clinician network
4, Victor Wei ZHANG, M.D., Ph.D. Assistant professor at the Baylor College of Medicine, ABMG Certified Clinical Molecular and Biochemical Geneticist
Responsibility: leading the working group to recruit and educate the volunteers from universities and hospitals
5, Zhiyu PENG, Ph.D. Expert in Bioinformatics, Chief Officer on clinical research and product development in BGI
Responsibility: leading the working group to organize genetic labs to utilize CHPO as clinical report standard
6, Ning LI, Ph.D. Steering committee member of international rare disease research consortium (IRDiRC), Steering committee member of Genome Denmark

Wiki Website and Search Engine Design & Maintenance Team: Weihong GU, Kai WANG, Ying ZHU, Lin ZHANG, Jianhu QIN,Hui HUANG,Wei ZHANG

HPO Communication Team: Ning LI, Kai WANG, Weihong GU, Yongping LI, Lin ZHANG

Mandate of the Steering Committee

The CHPO Steering Committee: 1. Adopts CHPO policies and guidelines 2. Coordinates efforts with non-profit organizations to address identified CHPO platform priorities e.g. as proposed by the working group 3. Monitors progress and provides updates to Co-Chairs 4. Agrees on a communication strategy that ensures timely and correct dissemination regarding CHPO objectives and progress made 5. Provides a forum for resolution of any conflicts, should they arise 6. Addresses gaps in communication with the working groups 7. Ensures non-conflict of interest against the basic research community and patient organizations

病人宣传团体联盟

CHPO指导委员会将邀请病人宣传团体的联盟组织代表参加委员会工作。这些团体组织应该代表广大病患的权益,无论他们身患何病,身处何地。

Umbrella organizations of patient advocacy groups

The CHPO Steering Committee invites representatives of umbrella organizations of patient advocacy groups to serve on the Committee. These umbrella organizations should represent broad patients' interests for a wide variety of diseases and geographical area.

观察员与咨询机构代表

经指导委员会成员提议,并经过委员会讨论达成一致意见,可以邀请观察员或可能成为顾问的机构代表(如监管机构)参加会议。

Observers and Representatives of Advisory Bodies

Upon proposal from a member, the Steering Committee can decide to invite observers to its meetings or representatives of organizations that may be given an advisory role, such as regulatory bodies. Such invitations shall be issued by the Chair in consultation with the members of the Steering Committee.

会议和程序规则

指导委员会会议至少每季度一次。李宁负责召集会议并依据指导委员会其他成员的议案来筹备并安排会议议程。 指导委员会致力于通过共识做出决议。如果一个决议没有达成共识,将通过参会代表举手表决、少数服从多数的原则形成决议。 指导委员会表决权成员参会人数达到50%方被认为构成法定人数。如无法达到法定人数,委员会主席需通过提前投票的方式以使参会人数满足法定要求(如无法参会,则可通过e-mail提前投票)。此类票数不及于参会人以明示或默示方式做出书面投票的票数。 指导委员会能够通过电子邮件(书面程序)执行决议,除非有任何成员由于某种原因反对使用该程序。在书面程序中,大多数成员需要给出积极或默许的意见,以使决策有效。 除非有正当理由,任何会议决定的全部条款应该至少在会议日期14个自然日之前传递给指导委员会成员。在最后的会议议程被采纳前,大多数的委员会成员仍然可同意紧急事务列入讨论议程并待决议。

Meetings and Rules of procedure

The Steering Committee meets at least once per quarter. Ning Li from BGI calls the meetings and prepares the meeting agenda with input from the other Committee members.

The Steering Committee aims to take decisions by consensus. If a decision cannot be reached by consensus, it is reached through a majority vote, based on the number of members present at the respective meeting.

In a meeting, the participation of 50% of the voting members of the Steering Committee is considered to constitute a quorum. If a quorum cannot be reached at a meeting, the Chair of the Committee seeks prior input from enough members to constitute a quorum (for instance e-mail voting ahead of time should Steering Committee members be unavailable at the date of the meeting). This input may be limited to the active or tacit agreement of a decision taken by the members present at the meeting and those having sent their written input.

The Steering Committee can take decisions by e-mail (written procedure) unless any member opposes the use of this procedure with regard to a particular matter. In a written procedure, a majority of members needs to give their active or tacit approval to render the decision valid.

Unless an exception to the rule can be duly justified, all items for decision at any given meeting should be communicated to the Steering Committee members at least fourteen calendar days in advance of the meeting date. A majority of the Committee members may nonetheless agree that urgent matters be tabled for discussion and decision at a meeting until the adoption of the final meeting agenda.

保密与无利益冲突

指导委员会的所有成员须签署保密和无利益冲突声明。 指导委员会成员不得以个人或机构代表的名义,在履行CHPO的职责过程中获取不当利益或不当利用影响力。 指导委员会成员可以根据CHPO的目标以个人或机构代表的名义参与资助项目,成员可以CHPO的目标来参与评估或筛选资助的提案。 然而,无论成员或其所属组织的已经提交或将要提交的,会议日程中所有与资助提案实际或潜在相关的事项都应该在无不当延误的情况下通知指导委员会主席。指导委员会主席确保妥当的处理关于任何潜在利益冲突问题。委员会成员可被要求从商议中弃权和/或从相关的条目/项目的讨论中回避。 此外,指导委员会成员需向主席报告任何实际或潜在、直接或间接可能使其无法公正履职的事由。 当指导委员会成员违反上述规定的要求,将考虑不再让他/她担任组织成员。

Confidentiality and Non Conflict of Interests

All members of the Steering Committee sign confidentiality and non-conflict of interest declarations.

Members of the Steering Committee shall not seek or act in any way, either in their personal capacity or as a representative of organization, as to take undue advantage of, or exercise undue influence on, any aspects regarding the implementation of CHPO.

Members of the Steering Committee may participate in projects funded according to CHPO objectives, either in their personal capacity or as a representative of organizations to which they belong. They may also participate in the evaluation or selection of proposals for funding according to CHPO objectives.

However, should any item on the agenda in a given meeting be of any relevance, actual or potential, for a proposal for funding that a member, or the organization to which he/she belongs, has submitted or is likely to submit, the member shall inform the Chair of the Steering Committee of the situation without undue delay. The Chair of the Steering Committee ensures the appropriate handling of any potential conflict of interest. The Committee member can be requested to abstain from the deliberations and/or leave the room for the discussion of the concerned item/subject.

Moreover, the Steering Committee members inform the Chair of any interests, actual or potential, explicitly or not explicitly stated above, which may be considered as prejudicial to their role on the Committee. When a member of the Steering Committee is in breach of the requirements set out above, he/she shall be considered as no longer being in a position to continue his/her duties as a member of the group.

透明性

成员应该遵守指导委员会会议讨论的机密性。 指导委员会成员名单将通过CHPO网站公开。会议的总结报告将公布在CHPO官方网站上,指导委员会另有决议的除外。

Transparency

The members should respect the confidential character of the discussions at the Steering Committee meetings. The names of the members of the Steering Committee are made public via the CHPO website. Summary reports from the meetings are published on the CHPO website unless the Steering Committee decides otherwise.