About Phenomics

Phenomics

Overview and identity

Phenomics is an English-language journal of human phenomics published by Springer since 2021, based in Shanghai, China. It carries the print ISSN 2730-583X and the electronic ISSN 2730-5848, appears under Springer's journal number 43657, and holds its copyright in the International Human Phenome Institutes (Shanghai), the Fudan University-led body behind the International Human Phenome Project. Springer describes it as a hybrid journal — authors may publish through the traditional route or open access — focusing on cutting-edge scientific advances in the emerging field of phenomics.

The title must be distinguished from Plant Phenomics, a different journal associated with Nanjing Agricultural University and published through Elsevier and Science Partner Journals, with different ISSNs, a different sponsor and a plant-science scope. Phenomics, without qualification, is the Shanghai human-science title: the journal of the measurable traits of individuals and populations, of phenotype measurement, phenome-wide association and precision medicine. Its founding editor-in-chief is Li Jin of Fudan University, whose 2021 editorial “Welcome to the Phenomics Journal” launched the title.

The field: phenome, phenotype and phenomics

The journal's founding editorial defines its terms carefully. The word “phenomics” was first coined by Steven A. Garan in 1996 and describes the measurement of phenomes. A phenome is a set of measurable traits — physical, chemical and biological phenotypes of individuals and populations — that result from the complex interactions of genes, epigenetics, symbiotic microorganisms, diet and environmental exposures. Phenomics is therefore the systematic, high-throughput study of those traits at every level, from the proteome and metabolome at the molecular level to the health and disease states of whole organisms.

The rationale for a dedicated journal follows from that definition. Genomics had acquired powerful journals, methods and databases over three decades, but the phenotype — the layer at which disease is actually experienced, diagnosed and treated — was measured less systematically and published, as Li Jin noted, mainly in broad-based biological journals. With high-efficiency integrated phenotyping facilities and international collaborative projects being deployed to study phenotypes systematically, there was, in the editorial's words, an urgent need for a publication forum that would specifically serve this scientific community. Phenomics was founded to be that forum, and later scholarly reviews describe it as the first international journal focusing on studies of human phenomes.

The International Human Phenome Project and its institutes

The journal is inseparable from the research programme that created it. Fudan University initiated the International Human Phenome Project in 2018 — Li Jin has led its first phase since 2017 in some institutional accounts — as a Chinese-led international “big science” initiative to measure human phenotypes precisely and analyse the human phenome comprehensively. The International Human Phenome Consortium was co-founded in 2018 by Li Jin of Fudan University, Jeremy Nicholson of Murdoch University in Australia and Leroy Hood of the Institute for Systems Biology in the United States, with a board of prestigious scholars from some twenty countries acting as its steering committee.

The consortium works through committees on technology and standards, on ethics, law and societal issues, and on data sharing, devoted to harmonised protocols for standardised phenotyping measurement and data processing. Its secretariat was formally established at the International Human Phenome Institutes (Shanghai) — the journal's copyright holder — and the institutes, together with the Human Phenome Institute of Fudan University, run the programme's infrastructure. Funded by the Shanghai municipal government, Fudan built what it describes as the world's first trans-scope, large-scale, multi-dimensional phenotyping platform at its Zhangjiang campus in Pudong, working across fifteen categories and more than 20,000 phenotypes, and the project's first phase, from 2018 to 2022, compiled a Human Phenome Atlas of associations between more than 1.5 million phenotypes. The second phase was launched in November 2023. Phenomics is the publishing organ of that enterprise: the place where its methods, standards and findings, and those of the worldwide community it convenes, enter the permanent literature.

Scope and topics of interest

Springer's description states that the journal welcomes studies advancing knowledge of phenomics — the study of the phenome as a set of measurable properties of physical, chemical and biological phenotypes of individuals and populations other than the genome. Its founding editorial lists topics of interest including high-throughput phenotyping and technological innovation; linking the genome to the phenome with models, algorithms and databases; exploring the relationships between phenotypes and understanding phenotypic variation; the precise application of phenomics in clinical disease, treatment, prevention and control; phenome-related multi-omics studies; phenome-related model organism research; and interdisciplinary, multiscale research.

The editorial also situated the field across functional genomics, pharmaceutical science, biomedical engineering, phylogenetics and disease genomics in humans and model organisms, covering both fundamental and applied research in the life sciences. In practice, then, the journal accepts work that measures phenotypes, work that explains phenotypes genetically or environmentally, work that associates phenotypes with each other and with disease — including phenome-wide association studies, the systematic counterpart of genome-wide association studies — and work that turns phenotypic knowledge into precision medicine, in which diagnosis, prognosis and drug choice are fitted to the measured characteristics of the individual patient.

Article types, frequency and the Protocol innovation

The founding editorial announced that the journal would consider articles, reviews, commentaries, brief communications and correspondences, and would publish online every two months. To those established forms the journal later added a less common one: a journal update announced that Phenomics had begun to accept Protocol as a new article type. Protocols must be original and already validated, must fall within the journal's scope, are peer-reviewed to high standards, and would normally run to less than 10,000 words with no upper word-count limit.

The addition of protocols is a small detail that reveals the journal's function. A field built on standardised measurement lives or dies by whether other laboratories can reproduce its measurements exactly, and the consortium behind the journal maintains a committee devoted to standard operating procedures for phenome studies. Publishing validated protocols as citable, peer-reviewed articles gives the scientists who write those procedures academic credit for them and gives the community a stable reference to follow. The journal has also recruited a Youth Editorial Board, offering distinguished young scholars a route into its editorial work — an investment in the next generation of a field that is itself young.

Research in the journal: from atlases to drug response

The journal's published research shows its scope in action across scales. At the population scale it has published phenome-wide association analysis revealing novel links between genetically determined levels of liver enzymes and disease phenotypes — a study design that starts from a genetic or molecular exposure and scans the phenome for consequences, inverting the usual disease-first logic of clinical research. At the organisational scale, its pages carry the reports of the International Human Phenome Consortium's board meetings, recording decisions on priorities that included the phenomics of major diseases, the technology systems and research infrastructure for phenome research, and standard operating procedures.

At the clinical scale, a 2025 brief communication in the journal used the Chiglitazar-perturbed Human multi-Omics ProfilE cohort, built from phase three trials of the diabetes drug chiglitazar with 835 patients, to show that baseline plasma levels of the protein GPX3 predicted which patients with type 2 diabetes would respond to the drug, with the authors — based at Fudan's Human Phenome Institute and the International Human Phenome Institutes (Shanghai) — presenting GPX3 as a potential biomarker for treatment stratification and personalised therapy. A review on phenomic imaging, meanwhile, defined the use of imaging to visualise and measure anatomical structures, functions and metabolic processes across scales, in both healthy and abnormal traits, and to integrate those images with genomics, proteomics, immunomics and metabolomics. Together these papers span the journal's whole argument: measure everything measurable, associate it systematically, and use the result to treat patients more precisely.

Editorial leadership and community

Li Jin, the founding editor-in-chief, is an academician of the Chinese Academy of Sciences, a co-founder of the International Human Phenome Consortium, and a senior leader of Fudan University, where he has served as executive vice president and dean of Shanghai Medical College and leads the Human Phenome Institute's work. His dual role — leader of the International Human Phenome Project and editor of its journal — gives Phenomics the same programmatic character as a society journal: its editorial priorities and the research programme's priorities are openly aligned, and its founding editorial invited the community directly to join its editorial board and contribute manuscripts to mark, in its phrase, a new era of phenomics.

The journal states that it established an international editorial board of leading scientists covering the various areas of its scope and that it strives to achieve fair peer review. That internationality mirrors its consortium, whose network Fudan reports as having grown to involve institutions and teams in some twenty countries, including academician-led teams, with domestic partnership through the Human Phenome Consortium of China, comprising dozens of universities, institutes, hospitals and enterprises led by academicians of the Chinese academies. The International Symposium of Human Phenomics, convened by the consortium, is the field's principal summit, and the journal and the symposium reinforce each other as the community's twin institutions.

Indexing, identifiers and access

Springer's journal information page records the electronic ISSN 2730-5848 and print ISSN 2730-583X and lists the journal as abstracted and indexed in a wide range of services, including BIOSIS and Biological Abstracts, Baidu, CLOCKSS, CNKI, CNPIEC, Chemical Abstracts Service, Dimensions, EBSCO, the Emerging Sources Citation Index, Google Scholar, the Japanese Science and Technology Agency's services and Wanfang, among others. Inclusion in the Emerging Sources Citation Index places it within the Web of Science Core Collection's discovery system, while CNKI and Wanfang coverage ensures it is findable inside China's own scholarly infrastructure — a dual visibility appropriate to a Shanghai journal with a global consortium behind it.

As a hybrid journal, Phenomics offers both subscription-route publication and open-access publication on the Springer Nature Link platform, where its articles carry DOIs in the form 10.1007/s43657. That platform also hosts its calls for papers, journal updates and submission guidelines. Hybrid status suits its mixed community: large consortium projects can choose open access for maximum dissemination, while individual research groups without open-access funding can still publish in the field's specialist journal.

Readership and significance

The journal's readers are researchers in human genetics and genomics, multi-omics and systems biology, clinical epidemiology, biomedical engineering and precision medicine; the staff of phenotyping facilities and cohort studies; and clinicians and pharmaceutical researchers interested in biomarkers and treatment stratification. Its authorship is led by the Fudan and Shanghai phenome community that founded it, but its subject — how to measure and interpret the human phenome — belongs to a worldwide movement that includes national cohort and biobank programmes on several continents.

Assessed as a whole, Phenomics is best understood as the journal of a scientific programme that aspired to do for phenotypes what the Human Genome Project did for sequence: measure comprehensively, standardise rigorously, share internationally and convert the resulting atlas into better medicine. Since 2021 it has given that programme, and the wider phenomics community, a dedicated, indexed, Springer-published forum in Shanghai, with Li Jin as founding editor and the International Human Phenome Institutes (Shanghai) as its institutional home. In a directory of Chinese journals it stands as a clear case of a title created not to follow a field but to found one — and to keep Plant Phenomics, its Nanjing plant-science namesake, in a separate entry where it belongs.