Add 22 new terms for nucleic acid delivery methods and integration states

[Copilot]

Bulk NTR for nucleic acid delivery taxonomy under Transfection (EFO:0000726), covering viral/non-viral delivery methods and transgene integration states.

New terms (EFO_0920064–EFO_0920085)

Nucleic acid delivery method (EFO_0920064) — organizational class under transfection

• Viral transduction method (EFO_0920065) — organizational class
  • Stable viral transduction method (EFO_0920066) — organizational class
    • Lentivirus transduction (EFO_0920067)
    • Retrovirus transduction (EFO_0920068)
  • Transient viral transduction method (EFO_0920069) — organizational class
    • Adenovirus transduction (EFO_0920070)
    • Adeno-associated virus transduction (EFO_0920071)
    • Herpes virus transduction (EFO_0920072)
• Non-viral transfection method (EFO_0920073) — organizational class
  • Electroporation (EFO_0920074)
  • Nucleofection (EFO_0920075)
  • Lipofection (EFO_0920076)
  • Nanoparticle-based transfection (EFO_0920077)
  • Microinjection (EFO_0920078)
  • Optical transfection (EFO_0920079)
  • Sonoporation (EFO_0920080)

Nucleic acid integration state (EFO_0920081) — organizational class under transfection

• Random locus integration (EFO_0920082)
• Targeted locus integration (EFO_0920083)
• Native locus replacement (EFO_0920084)
• Not-integrative transgene expression (EFO_0920085)

Term metadata

All definitions, synonyms, and cross-references updated to match the curator-provided spreadsheet:

• Definitions: Replaced with exact text from the spreadsheet
• Synonyms: Updated per spreadsheet (e.g. "viral transfection", "lentiviral vector", "retroviral vector", "adenoviral vector", "AAV vector", "HSV vector", "optoinjection", "cellular sonication", "episomal expression", etc.)
• xrefs: Added MI:0704, BAO:0000245 (nucleic acid delivery method); BAO:0000246 (stable viral transduction); BAO:0000247 (transient viral transduction); MI:0711 (electroporation); MI:0717 (lipofection); MI:0712 (microinjection); NCIT:C41099 (nucleic acid integration state)
• PMID citations: DOIs from spreadsheet converted to PMIDs (PMID:33976969, 28944281, 30710128, 39533042, 32798742, 34767864, 31704145, 19338665, 20071742, 30472380)
• Label: EFO_0920077 renamed to "nanoparticle-based transfection" (old label kept as related synonym)
• organizational_class: true on all grouping nodes

Original prompt

---

This section details on the original issue you should resolve

<issue_title>[NTR] Request for new [general description] terms</issue_title>
<issue_description>### Completed template

EFO Bulk Term Request Template - NA delivery methods.xlsx

Any additional comments

Tree of proposed terms:

• Transfection EFO:0000726 - existing
  • Nucleic acid delivery method
    • Viral transduction method
      • Stable viral transduction method
        • Lentivirus transduction
        • Retrovirus transduction
      • Transient viral transduction method
        • Adenovirus transduction
        • Adeno-associated virus transduction
        • Herpes virus transduction
    • Non-viral transfection method
      • Electroporation
      • Nucleofection
      • Lipofection
      • Nano-particle mediated transfection
      • Microinjection
      • Optical transfection
      • Sonoporation
  • Nucleic acid integration state
    • Random locus integration
    • Targeted locus integration
    • Native locus replacement
    • Not-integrative transgene expression</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes [NTR] Request for new [general description] terms #2432

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[zoependlington]

@copilot please look into the changes to efo-edit.owl and why the ontology_qc is failing

[Copilot]

@copilot please look into the changes to efo-edit.owl and why the ontology_qc is failing

The root cause was that when I ran make normalize_src (which uses robot convert), I used a dummy empty imports/mondo_import.owl to work around the missing file. ROBOT loaded the ontology with the empty import and when it re-serialized, it dropped the owl:imports statement for mondo_import.owl from the ontology header.

Without this import, build/efo.owl was built without MONDO terms, causing 27 MONDO terms referenced in components/subclasses.owl to appear as "dangling" (with only owl:Thing as parent).

Fixed in commit 8c94821 by restoring <owl:imports rdf:resource="http://www.ebi.ac.uk/efo/imports/mondo_import.owl"/> to the correct position in the ontology header.

[zoependlington]

@copilot

please take into account the spreadsheet for these terms too, I have pasted it below

Term Label	Term definition	Definition Citation	Parent	Child terms	Synonyms	X-refs	Comment
Nucleic acid delivery method	Method by which nucleic acids are delivered or engineered into a cell.		EFO:0000726			MI:0704||BAO:0000245
Viral transduction method	Viral-based transfection, or more specifically known as transduction, involves using a viral vector to carry a specific nucleic acid sequence into a host cell.	https://doi.org/10.7717/peerj.11165	Defined above - Nucleic acid delivery method		Viral transfection
Stable viral transduction method	Stable transfection ensures long-term expression of a transgene by integrating the introduced DNA into the host genome, therefore, maintaining the expression even after replication.	https://doi.org/10.7717/peerj.11165	Defined above - Viral transduction method			BAO:0000246
Lentivirus transduction	Stable transfection method involving the transgene introduction into the cells of interest using engineered lentiviral particles.		Defined above - Stable viral transduction method		Lentiviral vector
Retrovirus transduction	Stable transfection method involving the transgene introduction into the cells of interest using engineered retroviral particles.		Defined above - Stable viral transduction method		Retroviral vector
Transient viral transduction method	Transient transfection is the introduction of foreign nucleic acids into eukaryotic cells resulting in temporary expression of the introduced genes, without integration into the host genome.	https://doi.org/10.7717/peerj.11165	Defined above - Viral transduction method			BAO:0000247
Adenovirus transduction	Transient transfection method involving the transgene introduction into the cells of interest using engineered adenoviral particles. Adenoviral particles can transduce both replicating and non-dividing cells. Adenoviral DNA does not integrate into the host genome, but rather, resides episomally in the host nucleus.	https://doi.org/10.1016/j.gendis.2017.04.001	Defined above - Transient viral transduction method		Adenoviral vector
Adeno-associated virus transduction	Transient transfection method involving the transgene introduction into the cells of interest using engineered adeno-associated virus (AAV) particles. AAV particles can transduce both replicating and non-dividing cells. Engineered AAV DNA does not integrate into the host genome, but rather, resides episomally in the host nucleus. In comparison to adenoviral vectors, AAVs have low immunogenicity and cytotoxicity.	https://doi.org/10.1038/s41573-019-0012-9	Defined above - Transient viral transduction method		Adeno-associated viral vector||AAV vector||AAV transduction
Herpes virus transduction	Transient transfection method involving the transgene introduction into the cells of interest using engineered Herpes simplex virus (HSV) particles. HSV particles can transduce both replicating and non-dividing cells. Engineered HSV DNA does not integrate into the host genome, but rather, resides episomally in the host nucleus. HSV vectors have comparatively large transgene capacity (approx. 30kB) and have low immunogenicity.	https://doi.org/10.1038/s41434-024-00500-x	Defined above - Transient viral transduction method		HSV vector||Herpes simplex viral vector||HSV transduction
Non-viral transfection method	Non-viral transfection methods rely on physical or chemical means to introduce nucleic acids into cells without the use of viral vectors. Non-viral transfection methods are often preferred for their safety and ease of use, as they do not involve the complexities and potential risks associated with viral vectors, at the cost of lower transfection efficiency and specificity.		Defined above - Nucleic acid delivery method
Electroporation	Electroporation is the process of using an electric pulse to introduce DNA into cells by creating temporary pores in the cell membrane, allowing for efficient gene delivery.	https://doi.org/10.1016/B978-0-12-374849-2.00010-0	Defined above - Non-viral transfection method			MI:0711
Nucleofection	Nucleofection is a type of specialized electroporation which is designed to deliver genetic material directly to the nuclei of cells.	https://doi.org/10.1016/j.addr.2021.114042	Defined above - Non-viral transfection method
Lipofection	Lipofection is a liposome-based transfection technique whereby the nucleic acid is encapsulated within a phospholipid vesicle that can either directly fuse with cell membranes or be endocytosed by a cell, allowing delivery of the genetic material to the cell.	https://doi.org/10.1016/B978-0-12-800511-8.00011-3	Defined above - Non-viral transfection method			MI:0717
Optical transfection	Nucleic acid delivery method which involves short low-power bursts of laser beam to create transient pores in the cell membrane to allow entry of genetic material to the cell.	https://doi.org/10.1186/1423-0127-16-36	Defined above - Non-viral transfection method		Optoinjection||Laser optoporation||Optotransfection||Phototransfection||Photoporation
Sonoporation	Sonoporation is a technique for delivering genetic material into cells using sonication. In this process, externally applied acoustic pressure waves create temporary pores in the cell membrane, enabling the genetic material to enter the cell.	https://doi.org/10.1016/j.biomaterials.2020.120282	Defined above - Non-viral transfection method		Cellular sonication
Microinjection	Microinjection is a method that enables introduction of exogenous genetic material (or other substances, such as proteins) directly into the cytoplasm or nucleus of individual cells using a micrometer-diameter pipette by piercing the cell and/or nuclear membrane under visual control.	https://doi.org/10.1016/j.biomaterials.2020.120282	Defined above - Non-viral transfection method			MI:0712
Nanoparticle-based transfection	Nanoparticle-mediated transfection is a method for delivering genetic material into cells using small (<100 nm in diameter) nanoparticles, which can encapsulate genetic material and facilitate its entry into the cell. The nanoparticles can be engineered to enhance cellular specificity, protect the genetic material from degradation, and release it once inside the cell.	https://doi.org/10.1016/j.semcancer.2019.10.020	Defined above - Non-viral transfection method
Nucleic acid integration state	The state of nucleic acid (DNA or RNA) being integrated into a host genome, often as a result of viral infection or genetic engineering.		Defined above - Nucleic acid delivery method			NCIT:C41099
Random locus integration	Random locus integration refers to the process where an exogenous genetic material is inserted into the host genome at an arbitrary, rather than a specific, location.		Defined above - Nucleic acid integration state
Targeted locus integration	Targeted locus integration refers to the process where an exogenous genetic material is inserted into the host genome at specifically pre-determined location using cell's homology-directed repair mechanisms. In contrast to the random locus integration approach, this minimises the risk of insertional mutagenesis and ensures more consistent transgene expression.	https://doi.org/10.1093/nar/gkp1234	Defined above - Nucleic acid integration state
Native locus replacement	Native locus replacement refers to the process where the exogenously introduced genetic material replaces the host's native genomic sequence. This is achieved by introducing double-stranded DNA breaks in the host genome using gene editing tools, such as CRISPR/Cas9 or TALENS, together with template DNA (often a corrected or modified version of the gene) flanked by homology arms to promote the sequence incorporation into the host's genome at a native locus by means of homology-directed repair.		Defined above - Nucleic acid integration state
Non-integrative transgene expression	Non-integrative transgene expression refers to the process where the foreign genetic material is expressed without being permanently incorporated into the host's genome. Instead, the transgene exists in the cell as a separate entity, usually in the form of an episome, plasmid, or mRNA.	https://doi.org/10.1016/j.gene.2018.11.069	Defined above - Nucleic acid integration state		Episomal expression

[Copilot]

@copilot

please take into account the spreadsheet for these terms too, I have pasted it below
...

Done in commit 300fb90. Updated all 22 terms to match the spreadsheet:

• Definitions replaced with the exact text from the spreadsheet
• Synonyms updated (e.g., "lentiviral vector", "retroviral vector", "viral transfection", "AAV vector", "HSV vector", "episomal expression", optical transfection synonyms, etc.)
• xrefs added: MI:0704, BAO:0000245 (nucleic acid delivery method), BAO:0000246 (stable viral transduction), BAO:0000247 (transient viral transduction), MI:0711 (electroporation), MI:0717 (lipofection), MI:0712 (microinjection), NCIT:C41099 (nucleic acid integration state)
• PMIDs added from spreadsheet DOIs: PMID:33976969, 28944281, 30710128, 39533042, 32798742, 34767864, 31704145, 19338665, 20071742, 30472380
• Label for EFO_0920077 renamed to "nanoparticle-based transfection" (old label kept as related synonym)