Guidelines for Human Phenotype and proteins

1. Human Phenotype Reporting

• Describe clinical and morphological findings using Human Phenotype Ontology (HPO) terms where possible.
• Report:
  • Age, sex, and relevant ethnic background (when scientifically justified).
  • Diagnostic criteria used (e.g., ICD-11 or DSM-5 codes if applicable).
  • Clinical severity scores, onset, and progression pattern.
• Use structured phenotype descriptions (eg, HP:0001250 Seizure instead of “fits” or “episodes”).
• Clearly differentiate between observed phenotype and inferred diagnosis.
• For genetic disorders, specify whether the phenotype was confirmed molecularly or clinically.

2. Gene, Variant & Protein Nomenclature

• Follow official naming conventions from the HUGO Gene Nomenclature Committee (HGNC) and UniProt.
• Report gene symbols in italic uppercase (e.g., BRCA1), and protein symbols in Roman uppercase (e.g., BRCA1 protein).
• Genetic variants must be described using the Human Genome Variation Society (HGVS) nomenclature (e.g., NM_007294.4:c.68_69delAG).
• Specify genome build or reference sequence used (e.g., GRCh38/hg38).
• Include accession numbers (NCBI Gene, UniProt, Ensembl, or RefSeq) where appropriate.

3. Protein Expression & Quantification

• Clearly describe the biological source of proteins (e.g., tissue, cell line, serum, biopsy sample).
• Identify antibodies used for detection by Research Resource Identifiers (RRIDs).
• For proteomic studies:
  • Report mass spectrometry settings, peptide thresholds, and database search parameters.
  • Use standardized formats such as mzML or mzIdentML for data reporting.
• Quantitative results should include normalization methods, controls, and replicate numbers.
• Whenever possible, link to publicly accessible data (e.g., Human Protein Atlas or PRIDE database).

4. Methods & Reproducibility

• Describe all experimental protocols in sufficient detail to permit replication.
• Include reagents, cell lines, antibodies, and software used with RRIDs (e.g., RRID:AB_1234567).
• Use MIAPE (Minimum Information About a Proteomics Experiment) for proteomics and MINSEQE for sequencing data when applicable.
• State whether results were confirmed in independent biological or technical replicates.

5. Data Deposition & Public Repositories

• Deposition in publicly accessible databases is encouraged or required depending on the dataset type:

Provide accession numbers for all deposited datasets and cite them in the “Data Availability Statement.”

6. Ethics, Consent & Privacy

• All studies involving human material or data must comply with the Declaration of Helsinki and local/national ethics regulations.
• Include IRB or Ethics Committee approval identifiers and statements of written informed consent.
• Do not include personally identifiable information or genomic data that can be traced to individuals unless explicit consent for publication has been obtained.
• Authors are encouraged to use controlled-access repositories for sensitive genetic or proteomic data.

7. Presentation Standards

• Figures showing protein bands or blots must include molecular weight markers and replicate validation.
• Proteomic tables should contain identifiers: protein name, UniProt ID, peptide count, fold-change, p-value, and localization (cytoplasmic, nuclear, membrane, etc.).
• Genetic or phenotypic tables should include HPO IDs, variant classification (pathogenic, likely benign, etc.), and zygosity.
• Use standard SI units and provide methods of quantification (e.g., western blot densitometry, ELISA, qRT-PCR).

8. References & Resources

• Human Phenotype Ontology (HPO). https://hpo.jax.org/
• Human Protein Atlas (HPA). https://www.proteinatlas.org/
• HUGO Gene Nomenclature Committee (HGNC). https://www.genenames.org/
• Human Genome Variation Society (HGVS). https://www.hgvs.org/
• PRIDE Proteomics Repository. https://www.ebi.ac.uk/pride/
• ICMJE Recommendations. https://www.icmje.org/