Terms for transposons

[oushujun]

What is this request referring to?

487

Parent	labels	Synonyms	about
SO:0000186	LTR/Copia	RLC, Ty1, Copia, LTR-Copia	LTR retrotransposon in the Copia superfamily
SO:0000186	LTR/Gypsy	RLG, Ty3, Gypsy, LTR-Gypsy	LTR retrotransposon in the Gypsy superfamily
SO:0000186	LTR/Bel-Pao	RLB, Bel/Pao	LTR retrotransposon in the Bel-Pao superfamily
SO:0000186	LTR/Retrovirus	RLR	Retrovirus with LTR structure
SO:0000186	LTR/ERV	RLE, HERV	Endogenous retrovirus with LTR structure
SO:0000189	DIRS		Dictyostelium intermediate repeat sequence
DIRS	DIRS/DIRS	RYD	Dictyostelium intermediate repeat sequence superfamily DIRS
DIRS	DIRS/Ngaro	RYN	Dictyostelium intermediate repeat sequence superfamily Ngaro
DIRS	DIRS/VIPER	RYV	Dictyostelium intermediate repeat sequence superfamily VIPER
SO:0000189	Penelope	RPP	Penelop retrotransposon
SO:0000194	LINE/R2	RIR	LINE superfamily R2
SO:0000194	LINE/RTE	RIT	LINE superfamily RTE
SO:0000194	LINE/Jockey	RIJ	LINE superfamily Jockey
SO:0000194	LINE/L1	RIL	LINE superfamily L1
SO:0000194	LINE/I	RII	LINE superfamily I
SO:0000206	SINE/tRNA	RST	SINE superfamily tRNA
SO:0000206	SINE/7SL	RSL	SINE superfamily 7SL
SO:0000206	SINE/5S	RSS	SINE superfamily 5S
SO:0000182	Crypton	DYC	Crypton transposons contain a tyrosine recombinase, as do some phages, IS and DIRS-like retrotransposons, but lack an RT domain.
SO:0000208	DNA/Tc1-Mariner	DTT, Tc1, Mariner, Stowaway, TcMar-Stowaway	TIR superfamily Tc1–Mariner
SO:0000208	DNA/hAT	DTA, Ac, Ds, Ac/Ds, hAT-Ac	TIR superfamily hAT
SO:0000208	DNA/Mutator	DTM, MuDR, Mu, MULE, MLE	TIR superfamily Mutator
SO:0000208	DNA/Merlin	DTE	TIR superfamily Merlin
SO:0000208	DNA/Transib	DTR	TIR superfamily Transib
SO:0000208	DNA/P	DTP, P-element	TIR superfamily P
SO:0000208	DNA/PiggyBac	DTB	TIR superfamily PiggyBac
SO:0000208	DNA/PIF-Harbinger	DTH, PIF, Harbinger, Tourist	TIR superfamily PIF–Harbinger
SO:0000208	DNA/CACTA	DTC, En, Spm, dSpm, CACTC, En-Spm, EnSpm, CMC-EnSpm	TIR superfamily CACTA

Relevant Publications https://www.nature.com/articles/nrg2165 https://pubmed.ncbi.nlm.nih.gov/26709091/

Thanks, Shujun Ou

[davidwsant]

Hi Shujun,

Thank you for writing these out. Unfortunately, the definitions are going to need more information to be able to distinguish between terms. For instance, other than the name there is no true difference between LTR/Copia and LTR/Gypsy. Could you please update your table with full definitions? I tried going through the first paper listed, but I am not an expert in this field and do not trust that my definitions will be sufficient. Here is an example of the first three definitions I made:

Parent	labels	Synonyms	Def
SO:0000186 (LTR_retrotransposon)	LTR/Copia	RLC, Ty1, Copia, LTR-Copia	LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.
SO:0000186 (LTR_retrotransposon)	LTR/Gypsy	RLG, Ty3, Gypsy, LTR-Gypsy	LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles, but in Gypsy this contains only the matrix protein. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.
SO:0000186 (LTR_retrotransposon)	LTR/Bel-Pao	RLB, Bel/Pao	LTR retrotransposons in the Bel-Pao superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.

Of note, even with reading the paper, I do not see any clear distinction between the following pairs: Bel-Pao and Gypsy; Retrovirus and ERV; any of the DIRS; Jockey and L1; and most of the TIRs. Could you please make sure the definitions include enough information to distinguish between the terms ASIDE from using the names in the definitions.

Thank you,

Dave Sant

[oushujun]

Hi Dave,

Below is the updated table. Please let me know if anything is missing.

Parent	labels	Synonyms	def	Ref
SO:0000186	LTR/Copia	RLC, Ty1, Copia, LTR-Copia	LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165
SO:0000186	LTR/Gypsy	RLG, Ty3, Gypsy, LTR-Gypsy	LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165
SO:0000186	LTR/Bel-Pao	RLB, Bel/Pao	LTR retrotransposons in the Bel-Pao superfamily similar to LTR/Gypsy and Retroviridae. Mainly described in metazoan genomes. This superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and env (in the case of retroviruses). GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. env is envelop protein.	https://www.nature.com/articles/nrg2165
SO:0000186	LTR/Retrovirus	RLR	LTR retrotransposons in the retrovirus superfamily similar to LTR/Gypsy and Bel-Pao. Mainly described in vertebrate animals. This superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and env (in the case of retroviruses). GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. env is envelop protein.	https://www.nature.com/articles/nrg2165
SO:0000186	LTR/ERV	RLE, HERV	Endogenous retrovirus are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses(Type D). FClass III families are similar to foamy viruses.	https://www.nature.com/articles/nrg2165
SO:0000186	LTR/unknown	RLX	LTR retrotransposon with uncertain classifications. It may contain coding elements including: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.
SO:0000194	LINE/R2	RIR	R2 elements are non-long terminal repeat (non-LTR) retrotransposons that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256348/
SO:0000194	LINE/RTE	RIT	RTE-1 elements contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified RT domain.	https://pubmed.ncbi.nlm.nih.gov/9729877/
SO:0000194	LINE/Jockey	RIJ	Jockey is a superfamily of non-LTR retrotransposons found only in Arthropoda. The full-length element is ~ 5 kb and contains two ORFs (open reading frames), ORF1 (568 aa) and ORF2 (916 aa), which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT).	https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0184-1
SO:0000194	LINE/L1	RIL	Long interspersed element-1 (LINE-1) is found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124830/
SO:0000194	LINE/I	RII	The LINE I superfamily is similar to the Jocky and LI superfamily, which encodes ORF1 (open reading frame 1) and ORF2 (including APE, Apurinic endonuclease; RT,Reverse transcriptase). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain.	https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-interspersed-nuclear-element
SO:0000194	LINE/unknown	RIX	Long interspersed element with uncertain classifications.
SO:0000206	SINE/tRNA	RST	Short interspersed elements originated from tRNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/
SO:0000206	SINE/7SL	RSL	Short interspersed elements originated from 7SL RNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/
SO:0000206	SINE/5S	RSS	Short interspersed elements originated from 5S rRNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/
SO:0000206	SINE/unknown	RSX	Short interspersed element with uncertain classifications.
SO:0000182	Crypton	DYC	Crypton is a superfamily of DNA transposons using tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules.	https://mobilednajournal.biomedcentral.com/articles/10.1186/1759-8753-2-12
SO:0000208	DNA/Tc1-Mariner	DTT, Tc1, Mariner, Stowaway, TcMar-Stowaway	Terminal inverted repeat transposon superfamily with the Tc1 transposasse. Its activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp.	https://link.springer.com/chapter/10.1007%2F978-3-642-79795-8_6
SO:0000208	DNA/hAT	DTA, Ac, Ds, Ac/Ds, hAT-Ac	Terminal inverted repeat transposon superfamily first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461711/
SO:0000208	DNA/Mutator	DTM, MuDR, Mu, MULE, MLE	Mutator is a superfamily of terminal inverted repeat (TIR) transposon. Mutator TIRs are usually long but are also highly divergent - sharing only terminal G…C nucleotides — or are absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification.	https://www.nature.com/articles/nrg2165
SO:0000208	DNA/Merlin	DTE	Terminal inverted repeat transposon superfamily DDE transposase. Elements in this superfamily creates 8-9 bp target-site duplication (TSD).	https://www.nature.com/articles/nrg2165
SO:0000208	DNA/Transib	DTR	Terminal inverted repeat (TIR) transposon of the superfamily Transib contains the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination61.	https://www.nature.com/articles/nrg2165
SO:0000208	DNA/P	DTP, P-element	P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain.	https://www.cell.com/fulltext/0092-8674(83)90133-2
SO:0000208	DNA/PiggyBac	DTB	The terminal inverted repeat (TIR) transposon superfamily piggyBac, which is primarily found in animals, favours insertion adjacent to TTAA.	https://www.nature.com/articles/nrg2165
SO:0000208	DNA/PIF-Harbinger	DTH, PIF, Harbinger, Tourist	Terminal inverted repeat transposon superfamily PIF-Harbinger creates 3-bp target site duplication that are mainly “TAA” or “TTA”. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Tourist is the non-autonomous element in this superfamily usually shorter than 600 bp. The terminal sequences for PIF/Harbinger/Tourist elements are “GGG/CCC…GGC/GCC” or “GA/GGCA…TGCC/TC”.	https://pubmed.ncbi.nlm.nih.gov/26709091/
SO:0000208	DNA/CACTA	DTC, En, Spm, dSpm, CACTC, En-Spm, EnSpm, CMC-EnSpm	This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are “CACTA/G…C/TAGTG”. CACTA elements generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions.	https://pubmed.ncbi.nlm.nih.gov/26709091/
SO:0000189	DIRS		Dictyostelium intermediate repeat sequence (DIRS) is a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. DIRS retrotransposons have inverted terminal repeats (ITRs).	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/
DIRS	DIRS/DIRS	RYD	DIRS is a superfamily in Dictyostelium intermediate repeat sequence (DIRS) non-LTR retrotransposons carrying Tyrosine recombinase (YR) retrotransposon protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. MT is DNA N-6-adenine-methyltransferase.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/
DIRS	DIRS/Ngaro	RYN	Ngaro is a superfamily in Dictyostelium intermediate repeat sequence (DIRS) non-LTR retrotransposons with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/
DIRS	DIRS/VIPER	RYV	VIPER is a superfamily in Dictyostelium intermediate repeat sequence (DIRS) non-LTR retrotransposons with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes.	https://www.sciencedirect.com/science/article/pii/S0166685105002987
SO:0000189	Penelope	RPP	Penelope is a subclass of non-LTR retrotransposons. Penelope contains structural features of TR, RT, EN. TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is a reverse transcriptase. EN, endonuclease.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681739/

Best, Shujun

[davidwsant]

Dear Shujun,

Thank you for taking the time to create detailed definitions to go along with each of these terms. I am going through them to double-check everything, but at first glance it looks like they are good and will all be added. Thanks.

Dave

[oushujun]

Dear Dave,

Thank you for taking the time to curate these terms and adding them to the system. Looking forward to adding them to my study.

Shujun

On Fri, Jun 19, 2020 at 4:44 PM David Sant notifications@github.com wrote:

Dear Shujun,

Thank you for taking the time to create detailed definitions to go along with each of these terms. I am going through them to double-check everything, but at first glance it looks like they are good and will all be added. Thanks.

Dave

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488#issuecomment-646871094, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4ND4CUTCOC4DDDWFLL3RXPL2RANCNFSM4NMSP7RA .

[davidwsant]

Hi Shujun,

Thank you for writing up definitions and adding links to publications. Over the last week or so I have been through all of this information very thoroughly. I am not, however, an expert in the field so I suggest that you review my changes thoroughly as well.

Here is a summary of the changes that I have made:

• If any of the terms were plural, I made them singular (if they were all singular then I changed nothing)
• I chose only one term for each. Dashes, slashes and hyphens are not used in names. They can sometimes be used in synonyms. Multiple synonyms can be used, but it is best to use only one term. For instance, I changed Tc1/mariner to just Tc1 and added mariner as a synonym.
• Most of the names you added have the parent term followed by a slash and then a term name. This is fine for submitting the request, but I have changed it for simplicity to see the whole term name here.
• I notice that most of these definitions come directly from the publications. The bits that were added just needed consistent grammar, so the grammar has been changed in a handful of locations (just to be consistent).
• I have looked through all of the publications and done my best to make sure they are all labeled correctly. Please double check to make sure that I have not accidentally changed a DNA transposon to "retrotransposon" or something erroneous. I have also tried to change names to "element" or "transposon" in the names to make it as consistent with the literature as possible.
• Many of the short acronyms were not present in the references. I only want to add the acronyms if they are commonly used. If I have removed any that you feel are still important, please point me to a publication and I can add the term as a synonym. Adding a synonym can also be done after the terms have been added, so this is not a rush.
• PMIDs - Thank you for providing links. This was very helpful. I had added the PMIDs because that is how I will annotate the ontology files. What you did was correct, I am just adding more info here for my own help.
• The reference for LINE_I_element is not a peer-reviewed publication but appears to be out of a textbook. It is not required that I add a reference, but I am having a difficult time finding any peer-review publications for this. I am hesitant to add this term without a reference. Do you think you could find a publication that I can reference?
• The term DIRS seems to be referred to as YR_retrotransposon in the publication you references, while DIRS is a sub-family. For this reason, the term name has been changed. All others should match what you suggested to start with.
• Terms for unknowns are not added to SO. Instead, the parent term is used. Below I have a table of terms that I do not believe should be added, along with the term that should be used when annotating these terms.

Parent term that should be used	Suggested name	Synonym	Definition
SO:0000186 (LTR_retrotransposon)	LTR/unknown	RLX	LTR retrotransposon with uncertain classifications. These retrotransposons may contain coding elements including: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.
SO:0000194 (LINE_element)	LINE/unknown	RIX	Long interspersed element with uncertain classifications.
SO:0000206 (SINE_element)	SINE/unknown	RSX	Short interspersed element with uncertain classifications.

Here are my new suggested names and definitions. If you have any suggested changes, please specify each change in your response so that it will be easy for me to update my notes. Thanks.

Parent	labels	Synonyms	def	Ref
SO:0000186 (LTR_retrotransposon)	Copia_LTR_retrotransposon	Copia LTR retrotransposon	LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Gypsy_LTR_retrotransposon	Gypsy LTR retrotransposon	LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Bel_Pao_LTR_retrotransposon	Bel-Pao LTR retrotransposon	LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Retrovirus_LTR_retrotransposon	Retrovirus LTR retrotransposon	LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Endogenous_Retrovirus_LTR_retrotransposon	Endogenous Retrovirus LTR retrotransposon, ERV LTR retrotransposon	Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses(Type D). F-Class III families are similar to foamy viruses.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000194 (LINE_element)	R2_retrotransposon	R2 retrotransposon	R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256348/	PMID: 21734471
SO:0000194 (LINE_element)	RTE_element	RTE retrotransposon	RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain.	https://pubmed.ncbi.nlm.nih.gov/9729877/	PMID: 9729877
SO:0000194 (LINE_element)	LINE_Jockey_element	LINE Jockey element	Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT).	https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0184-1	PMID: 31709017
SO:0000194 (LINE_element)	L1_element	LINE-1 element, LINE 1 element, L1 element	Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124830/	PMID: 21801021
SO:0000194 (LINE_element)	LINE_I_element	LINE I element	Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain.	https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-interspersed-nuclear-element	***
SO:0000206 (SINE_element)	tRNA_SINE_element	tRNA SINE element	Short interspersed elements that originated from tRNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/	PMID: 21673742
SO:0000206 (SINE_element)	7SL_SINE_element	7SL element, 7SL SINE element	Short interspersed elements that originated from 7SL RNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/	PMID: 21673742
SO:0000206 (SINE_element)	5S_SINE_element	5S element, 5S SINE element	Short interspersed elements that originated from 5S rRNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/	PMID: 21673742
SO:0000182 (DNA_transposon)	Crypton_transposon	Crypton transposon	Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules.	https://mobilednajournal.biomedcentral.com/articles/10.1186/1759-8753-2-12	PMID: 22011512
SO:0000208 (terminal_inverted_repeat_element)	Tc1_transposon	Tc1 transposon, mariner transposon, mariner_transposon	Elements of the Tc1 Ttrminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp.	https://link.springer.com/chapter/10.1007%2F978-3-642-79795-8_6	PMID: 8556864, PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	hAT_transposon	hAT transposon	The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461711/	PMID: 11454746
SO:0000208 (terminal_inverted_repeat_element)	Mutator_transposon	Mutator transposon	Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent - sharing only terminal G…C nucleotides — or are absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	Merlin_transposon	Merlin transposon	Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD).	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	Transib_transposon	Transib, transib transposon	Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	P_transposable_element	P element, P-element, P transposable element	P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain.	https://www.cell.com/fulltext/0092-8674(83)90133-2	PMID: 6309410
SO:0000208 (terminal_inverted_repeat_element)	piggyBac_element	PiggyBac transposable element	Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements  favour insertion adjacent to TTAA.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	PIF_transposable_element	PIF transposon element, Harbinger transposon element, Tourist transposon element, DTH transposon element	Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly “TAA” or “TTA”. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are “GGG/CCC…GGC/GCC” or “GA/GGCA…TGCC/TC”.	https://pubmed.ncbi.nlm.nih.gov/26709091/	PMID: 26709091
SO:0000208 (terminal_inverted_repeat_element)	CACTA_transposable_element	CACTA transposon element, DTC transposon element, En transposon element, Spm transposon element, dSPM transposon element	This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are “CACTA/G…C/TAGTG”.	https://pubmed.ncbi.nlm.nih.gov/26709091/, https://www.sciencedirect.com/science/article/pii/S1874939915002692?via%3Dihub	PMID: 26709091
SO:0000189 (non_LTR_retrotransposon)	YR_retrotransposon	YR retrotransposon, tyrosine kinase retrotransposon	Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. retrotransposons have inverted terminal repeats (ITRs).	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/	PMID: 24086727
YR_retrotransposon	DIRS_retrotransposon	DIRS retrotransposon	Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:add ID) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/	PMID: 24086727
YR_retrotransposon	Ngaro_retrotransposon	Ngaro retrotransposon	Ngaro retrotransposons are members of the YR_retrotransposon (SO: add ID) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/	PMID: 24086727
YR_retrotransposon	Viper_retrotransposon	Viper retrotransposon	VIPER retrotransposons are members of the YR_retrotransposon (SO:add ID) superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes.	https://www.sciencedirect.com/science/article/pii/S0166685105002987	PMID: 16297462
SO:0000189 (non_LTR_retrotransposon)	Penelope_retrotransposon	Penelope retrotransposon	Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681739/	PMID: 23914310

I hope that this covers everything. This is getting close, but I would just like you to review the changes I suggested to ensure I did not make mistakes.

Thank you,

Dave Sant

[oushujun]

Dear Dave,

Thank you for curating these terms. I like most of them which are well-formatted and consistent. Here is the summary of changes I made:

• The diversity of synonyms reflects the rich history of this field and most of them should be retained but not just the most used ones. The 3-letter naming system was proposed by Wicker et al. 2007 to unify the diverse naming and has been used in many studies.
• LTR/SINE/LINE/TIR/YR strings are critical information in the label to provide structural information and reduce confusion and thus added to the ones processing such features.
• Similarly, the transposon/retrotransposon string provides information regarding the transposition mechanism and also added to the label.
• Some superfamilies, i.e., Tc1_Mariner, Bel_Pao, and PIF_Harbinger are traditional naming schemes that usually come together. The two parts of the name come from two separate families together define the superfamily.
• The descriptions look good. I just fixed some typos and formatting issues.
• The LINE I superfamily is not commonly seen. I added them for completeness. It's up to you to keep this or not.
• It's OK to remove the unknown entries.

This is the revised table. Thanks again for working on this issue. Please let me know if you want to change anything.

Parent	labels	Synonyms	def	Ref
SO:0000186 (LTR_retrotransposon)	Copia_LTR_retrotransposon	RLC, Ty1, Copia LTR retrotransposon	LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Gypsy_LTR_retrotransposon	RLG, Ty3, Gypsy LTR retrotransposon	LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Bel_Pao_LTR_retrotransposon	RLB, Bel-Pao LTR retrotransposon	LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Retrovirus_LTR_retrotransposon	RLR, retrovirus LTR retrotransposon	LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000186 (LTR_retrotransposon)	Endogenous_Retrovirus_LTR_retrotransposon	RLE, HERV, Endogenous Retrovirus LTR retrotransposon	Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses (Type D). F-Class III families are similar to foamy viruses.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000194 (LINE_element)	R2_LINE_retrotransposon	RIR, R2 retrotransposon	R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256348/	PMID: 21734471
SO:0000194 (LINE_element)	RTE_LINE_retrotransposon	RIT, RTE retrotransposon	RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain.	https://pubmed.ncbi.nlm.nih.gov/9729877/	PMID: 9729877
SO:0000194 (LINE_element)	Jockey_LINE_retrotransposon	RIJ, LINE Jockey element	Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT).	https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-019-0184-1	PMID: 31709017
SO:0000194 (LINE_element)	L1_LINE_retrotransposon	RIL, LINE-1 element, LINE 1 element, L1 element	Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124830/	PMID: 21801021
SO:0000194 (LINE_element)	I_LINE_retrotransposon	RII, LINE I element	Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain.	https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-interspersed-nuclear-element	***
SO:0000206 (SINE_element)	tRNA_SINE_retrotransposon	RST, tRNA SINE element	Short interspersed elements that originated from tRNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/	PMID: 21673742
SO:0000206 (SINE_element)	7SL_SINE_retrotransposon	RSL, 7SL SINE element	Short interspersed elements that originated from 7SL RNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/	PMID: 21673742
SO:0000206 (SINE_element)	5S_SINE_retrotransposon	RSS, 5S SINE element	Short interspersed elements that originated from 5S rRNAs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242629/	PMID: 21673742
SO:0000182 (DNA_transposon)	Crypton_YR_transposon	DYC, Crypton transposon	Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules.	https://mobilednajournal.biomedcentral.com/articles/10.1186/1759-8753-2-12	PMID: 22011512
SO:0000208 (terminal_inverted_repeat_element)	Tc1_Mariner_TIR_transposon	DTT, Tc1, Mariner, Stowaway, TcMar-Stowaway transposon	Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp.	https://link.springer.com/chapter/10.1007%2F978-3-642-79795-8_6	PMID: 8556864, PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	hAT_TIR_transposon	DTA, Ac, Ds, Ac/Ds, hAT-Ac, hAT transposon	The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461711/	PMID: 11454746
SO:0000208 (terminal_inverted_repeat_element)	Mutator_TIR_transposon	DTM, MuDR, Mu, MULE, MLE, Mutator transposon	Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent - sharing only terminal G…C nucleotides — or are absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	Merlin_TIR_transposon	DTE, Merlin transposon	Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD).	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	Transib_TIR_transposon	DTR, transib transposon	Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	P_TIR_transposon	DTP, P-element, P element, P-element, P transposable element	P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain.	https://www.cell.com/fulltext/0092-8674(83)90133-2	PMID: 6309410
SO:0000208 (terminal_inverted_repeat_element)	piggyBac_TIR_transposon	DTB, PiggyBac transposable element	Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements favour insertion adjacent to TTAA.	https://www.nature.com/articles/nrg2165	PMID: 17984973
SO:0000208 (terminal_inverted_repeat_element)	PIF_Harbinger_TIR_transposon	DTH, PIF, Harbinger, Tourist transposon element	Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly “TAA” or “TTA”. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are “GGG/CCC…GGC/GCC” or “GA/GGCA…TGCC/TC”.	https://pubmed.ncbi.nlm.nih.gov/26709091/	PMID: 26709091
SO:0000208 (terminal_inverted_repeat_element)	CACTA_TIR_transposon	DTC, En, Spm, dSpm, CACTC, En-Spm, EnSpm, CMC-EnSpm, CACTA transposon element	This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are “CACTA/G…C/TAGTG”.	https://pubmed.ncbi.nlm.nih.gov/26709091/, https://www.sciencedirect.com/science/article/pii/S1874939915002692?via%3Dihub	PMID: 26709091
SO:0000189 (non_LTR_retrotransposon)	YR_retrotransposon	YR retrotransposon, tyrosine kinase retrotransposon	Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. YR retrotransposons have inverted terminal repeats (ITRs).	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/	PMID: 24086727
YR_retrotransposon	DIRS_YR_retrotransposon	RYD, DIRS retrotransposon	Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:add ID) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/	PMID: 24086727
YR_retrotransposon	Ngaro_YR_retrotransposon	RYN, Ngaro retrotransposon	Ngaro retrotransposons are members of the YR_retrotransposon (SO: add ID) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783388/	PMID: 24086727
YR_retrotransposon	Viper_YR_retrotransposon	RYV, Viper retrotransposon	VIPER retrotransposons are members of the YR_retrotransposon (SO:add ID) superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes.	https://www.sciencedirect.com/science/article/pii/S0166685105002987	PMID: 16297462
SO:0000189 (non_LTR_retrotransposon)	Penelope_retrotransposon	RPP, Penelope retrotransposon	Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681739/	PMID: 23914310

Best, Shujun

[davidwsant]

Hi Shujun,

Thank you for looking through this thoroughly. I am glad that you were able to catch the things that needed to be changed. I noticed that you changed some terms from "element" to "retrotransposon", and I am glad you are more familiar with these than I am so that you know which ones to change. The publications tend to mention the class and then leave the individual superfamilies with just the short name, but I would prefer to include the longer name because it is more specific yet I want to be as consistent with the literature as possible. I think keeping the "I Line" is fine. I will add the link, but no PubMed ID. I think this looks good and I am just about ready to add the terms.

I only have one more thing to ask. As for the three-letter names, if these are well known then they should be included as you have suggested. However, any three-letter acronym has likely been used elsewhere and some of them are likely to match up with other scientific terms. The two-letter names are even more likely to be an acronym for something else. Do you think I could put the type of transposon with the synonym just to make it easier? For instance, it could be "RLC retrotransposon" instead of RLC. Would that be acceptable?

Here is a list of some well-known acronyms that happen to match synonyms included here:

• RLE: Right Lower Extremity
• RST: Rapid Strep Test
• DTT: dithiothreitol, a chemical commonly used as a reducing reagent in labs
• DPT: Diptheria-pertussis-tetanus vaccine
• Ds: Double-stranded. If you type this one into the SO Broswer it will give you ds-DNA.
• hAT: histone acetyltransferase
• Ac: Acetylation, as in histone acetylation. The most commonly known one is H3K37Ac. These have not been added to SO, but it has been discussed.
• Mu: The greek letter. This is used for many things including 'micro', so I especially don't want this one used alone
• En: English, as in using the English version of something

Aside from these ones that have other meanings known among scientists, there are many other meanings that are commonly used in everyday occurrences, especially in shorthand versions of text from younger generations. I think it would be best if we added something to the synonym for all of the two or three letter symbols to avoid confusion. Would that be ok with you?

Below are the term names and the suggested changes I have for the synonyms:

labels	Synonyms
Copia_LTR_retrotransposon	RLC retrotransposon, Ty1 retrotransposon, Copia LTR retrotransposon
Gypsy_LTR_retrotransposon	RLG retrotransposon, Ty3 retrotransposon, Gypsy LTR retrotransposon
Bel_Pao_LTR_retrotransposon	RLB retrotransposon, Bel-Pao LTR retrotransposon
Retrovirus_LTR_retrotransposon	RLR retrotransposon, retrovirus LTR retrotransposon
Endogenous_Retrovirus_LTR_retrotransposon	RLE retrotransposon, HERV, Endogenous Retrovirus LTR retrotransposon
R2_LINE_retrotransposon	RIR retrotransposon, R2 retrotransposon
RTE_LINE_retrotransposon	RIT retrotransposon, RTE retrotransposon
Jockey_LINE_retrotransposon	RIJ retrotransposon, LINE Jockey element
L1_LINE_retrotransposon	RIL retrotransposon, LINE-1 element, LINE 1 element, L1 element
I_LINE_retrotransposon	RII retrotransposon, LINE I element
tRNA_SINE_retrotransposon	RST retrotransposon, tRNA SINE element
7SL_SINE_retrotransposon	RSL retrotransposon, 7SL SINE element
5S_SINE_retrotransposon	RSS retrotransposon, 5S SINE element
Crypton_YR_transposon	DYC transposon, Crypton transposon
Tc1_Mariner_TIR_transposon	DTT transposon, Tc1 transposon, Mariner, Stowaway, TcMar-Stowaway transposon
hAT_TIR_transposon	DTA transposon, Ac transposon, Ds transposon, Ac/Ds, hAT-Ac, hAT transposon
Mutator_TIR_transposon	DTM transposon, MuDR, Mu transposon, MULE, MLE transposon, Mutator transposon
Merlin_TIR_transposon	DTE transposon, Merlin transposon
Transib_TIR_transposon	DTR transposon, transib transposon
P_TIR_transposon	DTP transposon, P-element, P element, P-element, P transposable element
piggyBac_TIR_transposon	DTB transposon, PiggyBac transposable element
PIF_Harbinger_TIR_transposon	DTH transposon, PIF transposon, Harbinger, Tourist transposon element
CACTA_TIR_transposon	DTC transposon, En transposon, Spm transposon, dSpm, CACTC, En-Spm, EnSpm, CMC-EnSpm, CACTA transposon element
YR_retrotransposon	YR retrotransposon, tyrosine kinase retrotransposon
DIRS_YR_retrotransposon	RYD retrotransposon, DIRS retrotransposon
Ngaro_YR_retrotransposon	RYN retrotransposon, Ngaro retrotransposon
Viper_YR_retrotransposon	RYV retrotransposon, Viper retrotransposon
Penelope_retrotransposon	RPP retrotransposon, Penelope retrotransposon

Do these changes look ok?

Thanks,

Dave

[oushujun]

That's appropriate. Thanks for taking the causion of not confusing them with other acronyms.

Best, Shujun

On Thu, Jun 25, 2020 at 1:07 PM David Sant notifications@github.com wrote:

Hi Shujun,

Thank you for looking through this thoroughly. I am glad that you were able to catch the things that needed to be changed. I noticed that you changed some terms from "element" to "retrotransposon", and I am glad you are more familiar with these than I am so that you know which ones to change. The publications tend to mention the class and then leave the individual superfamilies with just the short name, but I would prefer to include the longer name because it is more specific yet I want to be as consistent with the literature as possible. I think keeping the "I Line" is fine. I will add the link, but no PubMed ID. I think this looks good and I am just about ready to add the terms.

I only have one more thing to ask. As for the three-letter names, if these are well known then they should be included as you have suggested. However, any three-letter acronym has likely been used elsewhere and some of them are likely to match up with other scientific terms. The two-letter names are even more likely to be an acronym for something else. Do you think I could put the type of transposon with the synonym just to make it easier? For instance, it could be "RLC retrotransposon" instead of RLC. Would that be acceptable?

Here is a list of some well-known acronyms that happen to match synonyms included here:

• RLE: Right Lower Extremity
• RST: Rapid Strep Test
• DTT: dithiothreitol, a chemical commonly used as a reducing reagent in labs
• DPT: Diptheria-pertussis-tetanus vaccine
• Ds: Double-stranded. If you type this one into the SO Broswer it will give you ds-DNA.
• hAT: histone acetyltransferase
• Ac: Acetylation, as in histone acetylation. The most commonly known one is H3K37Ac. These have not been added to SO, but it has been discussed.
• Mu: The greek letter. This is used for many things including 'micro', so I especially don't want this one used alone
• En: English, as in using the English version of something

Aside from these ones that have other meanings known among scientists, there are many other meanings that are commonly used in everyday occurrences, especially in shorthand versions of text from younger generations. I think it would be best if we added something to the synonym for all of the two or three letter symbols to avoid confusion. Would that be ok with you?

Below are the term names and the suggested changes I have for the synonyms: labels Synonyms Copia_LTR_retrotransposon RLC retrotransposon, Ty1 retrotransposon, Copia LTR retrotransposon Gypsy_LTR_retrotransposon RLG retrotransposon, Ty3 retrotransposon, Gypsy LTR retrotransposon Bel_Pao_LTR_retrotransposon RLB retrotransposon, Bel-Pao LTR retrotransposon Retrovirus_LTR_retrotransposon RLR retrotransposon, retrovirus LTR retrotransposon Endogenous_Retrovirus_LTR_retrotransposon RLE retrotransposon, HERV, Endogenous Retrovirus LTR retrotransposon

R2_LINE_retrotransposon RIR retrotransposon, R2 retrotransposon RTE_LINE_retrotransposon RIT retrotransposon, RTE retrotransposon Jockey_LINE_retrotransposon RIJ retrotransposon, LINE Jockey element L1_LINE_retrotransposon RIL retrotransposon, LINE-1 element, LINE 1 element, L1 element I_LINE_retrotransposon RII retrotransposon, LINE I element

tRNA_SINE_retrotransposon RST retrotransposon, tRNA SINE element 7SL_SINE_retrotransposon RSL retrotransposon, 7SL SINE element 5S_SINE_retrotransposon RSS retrotransposon, 5S SINE element

Crypton_YR_transposon DYC transposon, Crypton transposon Tc1_Mariner_TIR_transposon DTT transposon, Tc1 transposon, Mariner, Stowaway, TcMar-Stowaway transposon hAT_TIR_transposon DTA transposon, Ac transposon, Ds transposon, Ac/Ds, hAT-Ac, hAT transposon Mutator_TIR_transposon DTM transposon, MuDR, Mu transposon, MULE, MLE transposon, Mutator transposon Merlin_TIR_transposon DTE transposon, Merlin transposon Transib_TIR_transposon DTR transposon, transib transposon P_TIR_transposon DTP transposon, P-element, P element, P-element, P transposable element piggyBac_TIR_transposon DTB transposon, PiggyBac transposable element PIF_Harbinger_TIR_transposon DTH transposon, PIF transposon, Harbinger, Tourist transposon element CACTA_TIR_transposon DTC transposon, En transposon, Spm transposon, dSpm, CACTC, En-Spm, EnSpm, CMC-EnSpm, CACTA transposon element

YR_retrotransposon YR retrotransposon, tyrosine kinase retrotransposon DIRS_YR_retrotransposon RYD retrotransposon, DIRS retrotransposon Ngaro_YR_retrotransposon RYN retrotransposon, Ngaro retrotransposon Viper_YR_retrotransposon RYV retrotransposon, Viper retrotransposon Penelope_retrotransposon RPP retrotransposon, Penelope retrotransposon

Do these changes look ok?

Thanks,

Dave

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[davidwsant]

Hi Shujun,

After all that discussion and reading through all of those papers, the terms are finally added. The new terms have been assigned IDs SO:0002264-SO:0002290. I should also mention that the term P_element (SO:0001535) was already present, but it has been updated with the info from our discussion. The SO Browser updates once per day, so the changes should be visible on the page within approximately 24 hours. I hope this covers all of the terms that you need. If you find any more, go ahead and create a new issue.

Good luck with your project,

Dave Sant

[oushujun]

Hi Dave,

That's fantastic! Thanks for taking the time and great efforts to add these terms.

Best, Shujun