CHPO

來自中國HPO翻譯委員會
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Chinese Human Phenotype Ontology Consortium (CHPO)

中文人類表型標準用語聯盟

背景

隨著基因測序技術的發展,人們獲取自身基因組數據的途徑越來越便捷,科學研究的重點轉向了如何解讀這些基因組數據與人類疾病的關系。隨著對人類疾病研究的逐漸深入,科學家們越來越意識到臨床表型數據的重要性,將基因型與表型數據聯合分析,成為眾多疾病研究的一個方向。

然而目前在國內,大部分醫療、科研工作者所使用的表型描述詞語并沒有統一的標準,大多數醫院信息系統中記錄的臨床表型數據都是非結構化的自然語句,這對人類疾病、尤其是遺傳性疾病的臨床研究和交流帶來了不便,對后期的數據分析和挖掘也造成了很大的困擾,因此,在中國建立一套標準的臨床表型用語變得非常重要。

HPO(Human Phenotype Ontology,人類表型標準用語,人類表型本體)項目旨在提供一套描述人類疾病所致的異常表型的標準詞語集。目前HPO已收錄約11000個詞條,每個詞條對應一種異常表型,HPO對所有的詞條進行了系統的分類管理。為方便HPO在臨床、科研領域的應用,HPO對OMIM、Orphanet和DECIPHER中記錄的7000多種遺傳病提供了HPO注釋;同時,還為約4000種常見疾病提供了HPO注釋。此外,HPO開發組還在持續地進行詞條的維護和完善工作。

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建立過程中,2015年底,由華大基因團隊、美國醫學遺傳學學院會員張巍教授和南加州大學生物信息學專家王凱教授共同翻譯HPO詞條,王凱教授搭建了wiki網站;中日友好醫院顧衛紅教授在相關方協調溝通組織方面付出了很大的努力;北京協和醫學院黃尚志教授給予了大力的支持。2016年初,在華大基因楊煥明院士與HPO創始人Peter Robinson教授的推動下,成立了中文人類表型標準用語聯盟(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工作目標

CHPO是一個志愿參與的項目,旨在中國建立一個開放平臺, 聯合各相關領域專業人士,逐步建立中文臨床表型術語標準,并讓其指導、服務于中文使用者的臨床和科研工作。在此承諾CHPO與臨床機構、基礎研究機構、專業協會和患者組織無利益沖突,并致力于在2017年前實現兩個目標: 1. 提供人類表型的中文標準術語 2. 提供一個高效的中文人類表型搜索引擎

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由一個指導委員會、兩個工作組管理。這些機構的組成和授權如下所述:

CHPO指導委員會及維護組和HPO聯絡組

指導委員會主席 Peter Robinson教授和楊煥明教授是委員會聯席主席,主要職責包括指導委員會的召集和主持決議程序。

歐洲和美國成員:(由Peter Robinson教授提名)

總協調人:顧衛紅

中國成員

  • 黃尚志,國內知名遺傳學家,曾任北京協和醫學院遺傳室主任,世界衛生組織遺傳病社區控制合作中心主任,中國罕見病發展中心顧問
職責:向中國醫學院校宣傳推廣CHPO
  • 王凱,博士,哥倫比亞大學副教授,生物信息學專家
職責:開發CHPO編輯平臺和搜索引擎
  • 顧衛紅,博士,臨床遺傳專家,中日友好醫院神經內科運動障礙與神經遺傳病研究中心負責人,中國罕見病發展中心顧問
職責:在臨床醫療系統宣傳推廣CHPO
  • 張巍,博士,美國醫學遺傳學院專家委員,貝勒醫學院客座副教授,廣州嘉檢醫學主任,經美國醫學遺傳學會(ABMG)認證的臨床分子遺傳學與臨床生化遺傳學專家
職責:負責招募與教育來自大學和醫院的志愿者。
  • 彭智宇,博士,生物信息學專家,華大基因臨床研究和產品開發總負責人
職責:將CHPO作為臨床報告標準應用于遺傳實驗室
  • 李寧,博士,國際罕見病研究聯盟指導委員會委員,GenomeDenmark指導委員會委員
職責:在中國法律框架內優化倫理和監管流程,保護CHPO版權和品牌免于非授權的商業化,和負責CHPO指導委員會公共關系管理

Wiki網站和搜索引擎設計&維護組:顧衛紅、王凱、朱贏、張林、秦建虎、黃輝、張巍

HPO聯絡組:李寧、王凱、顧衛紅、李勇平、張林

CHPO指導委員會的授權

1. 制定CHPO的政策和指導方針 2. 與非營利性基金合作,解決CHPO評定的優先項目,如經由CHPO工作組確認的項目 3. 監督進度,向聯席主席報告進展 4. 商定傳播策略以確保及時、準確地宣傳委員會的目標與工作進展 5. 如果出現任何矛盾,將提供座談會協助解決 6. 推動加強各工作組之間的溝通 7. 確保與基礎研究團體和病人組織無利益沖突

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

病人宣傳團體聯盟

CHPO指導委員會將邀請病人宣傳團體的聯盟組織代表參加委員會工作。這些團體組織應該代表廣大病患的權益,無論他們身患何病,身處何地。

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.

觀察員與咨詢機構代表

經指導委員會成員提議,并經過委員會討論達成一致意見,可以邀請觀察員或可能成為顧問的機構代表(如監管機構)參加會議。

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.

會議和程序規則

指導委員會會議至少每季度一次。李寧負責召集會議并依據指導委員會其他成員的議案來籌備并安排會議議程。 指導委員會致力于通過共識做出決議。如果一個決議沒有達成共識,將通過參會代表舉手表決、少數服從多數的原則形成決議。 指導委員會表決權成員參會人數達到50%方被認為構成法定人數。如無法達到法定人數,委員會主席需通過提前投票的方式以使參會人數滿足法定要求(如無法參會,則可通過e-mail提前投票)。此類票數不及于參會人以明示或默示方式做出書面投票的票數。 指導委員會能夠通過電子郵件(書面程序)執行決議,除非有任何成員由于某種原因反對使用該程序。在書面程序中,大多數成員需要給出積極或默許的意見,以使決策有效。 除非有正當理由,任何會議決定的全部條款應該至少在會議日期14個自然日之前傳遞給指導委員會成員。在最后的會議議程被采納前,大多數的委員會成員仍然可同意緊急事務列入討論議程并待決議。

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.

保密與無利益沖突

指導委員會的所有成員須簽署保密和無利益沖突聲明。 指導委員會成員不得以個人或機構代表的名義,在履行CHPO的職責過程中獲取不當利益或不當利用影響力。 指導委員會成員可以根據CHPO的目標以個人或機構代表的名義參與資助項目,成員可以CHPO的目標來參與評估或篩選資助的提案。 然而,無論成員或其所屬組織的已經提交或將要提交的,會議日程中所有與資助提案實際或潛在相關的事項都應該在無不當延誤的情況下通知指導委員會主席。指導委員會主席確保妥當的處理關于任何潛在利益沖突問題。委員會成員可被要求從商議中棄權和/或從相關的條目/項目的討論中回避。 此外,指導委員會成員需向主席報告任何實際或潛在、直接或間接可能使其無法公正履職的事由。 當指導委員會成員違反上述規定的要求,將考慮不再讓他/她擔任組織成員。

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

成員應該遵守指導委員會會議討論的機密性。 指導委員會成員名單將通過CHPO網站公開。會議的總結報告將公布在CHPO官方網站上,指導委員會另有決議的除外。

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.