Name elements that indicate taxon is a virus #7

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KatjaSchulz opened this Issue May 13, 2015 · 4 comments

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It looks like names with these elements are not yet recognized as viruses, so capitalized words are stripped from the canonical form:

NPV, e.g., Papilio polyxenes NPV: http://eol.org/pages/41592578
RNA, e.g., Alternaria zinniae dsRNA element: http://eol.org/pages/11611917
virophage, e.g., Organic Lake virophage: http://eol.org/pages/20868817
satellites, e.g., Double-stranded RNA satellites: http://eol.org/pages/11603787
satellite, e.g., Whitefly VEM satellite: http://eol.org/pages/20858522
betasatellite, e.g., Tomato leaf curl China betasatellite: http://eol.org/pages/11603870
alphasatellite, e.g., Ageratum yellow vein Singapore alphasatellite: http://eol.org/pages/39738381
particle, e.g., Mouse Intracisternal A-particle: http://eol.org/pages/11609198
subgroup, e.g., Subgroup B: http://eol.org/pages/11623168 -- This is probably not limited to viruses, but it's very unlikely that any name that has this string in it will have author information associated with it.

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dimus May 13, 2015

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Thanks Katja, I will look at these words through GN names to see if I get some unexpected consequences (unlikely) and everything that is safe will go to the next version of parser

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dimus commented May 13, 2015

Thanks Katja, I will look at these words through GN names to see if I get some unexpected consequences (unlikely) and everything that is safe will go to the next version of parser

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RNA happens in surrogate names, so it is a bit dangerous to say everything that has RNA word are viruses, but probably is ok (if there are no other indications it is a virus) to just refuse to parse:

|Candida albicans RNA_12C-1 |
| Candida albicans RNA_12C-2 |
| Candida albicans RNA_12C-3 |
| Candida albicans RNA_CTR0-1 |
| Candida albicans RNA_CTR0-2 |
| Candida albicans RNA_CTR0-3 |
| Candida albicans RNA_GC75-1 |
| Candida albicans RNA_GC75-2 |
| Candida albicans RNA_GC75-3 |
| Candida albicans RNA_SC5314-1 |
| Candida albicans RNA_SC5314-2 |
| Candida albicans RNA_SC5314-3 |
| Candida tropicalis RNA_Ct1-1 |
| Candida tropicalis RNA_Ct1-2 |
| Candida tropicalis RNA_Ct2-1 |
| Candida tropicalis RNA_Ct2-2 |
| Candida tropicalis RNA_Ct3-1 |
| Candida tropicalis RNA_Ct3-2

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dimus commented May 13, 2015

RNA happens in surrogate names, so it is a bit dangerous to say everything that has RNA word are viruses, but probably is ok (if there are no other indications it is a virus) to just refuse to parse:

|Candida albicans RNA_12C-1 |
| Candida albicans RNA_12C-2 |
| Candida albicans RNA_12C-3 |
| Candida albicans RNA_CTR0-1 |
| Candida albicans RNA_CTR0-2 |
| Candida albicans RNA_CTR0-3 |
| Candida albicans RNA_GC75-1 |
| Candida albicans RNA_GC75-2 |
| Candida albicans RNA_GC75-3 |
| Candida albicans RNA_SC5314-1 |
| Candida albicans RNA_SC5314-2 |
| Candida albicans RNA_SC5314-3 |
| Candida tropicalis RNA_Ct1-1 |
| Candida tropicalis RNA_Ct1-2 |
| Candida tropicalis RNA_Ct2-1 |
| Candida tropicalis RNA_Ct2-2 |
| Candida tropicalis RNA_Ct3-1 |
| Candida tropicalis RNA_Ct3-2

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dimus May 14, 2015

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I am not sure what to do with subgroup. Here are some examples:

xLevivirus subgroup I
plant rhabdoviruses subgroup B
Zelotes mayanus subgroup
Teuchophorus notabilis subgroup Meuffels & Grootaert 2004
Subgroup I Geminivirus
Sericania mimica subgroup Kobayashi & Fujioka 2008
Pipistrellus (Hypsugo) imbricatus subgroup

I will leave subgroup as is until I understand how to deal with it

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dimus commented May 14, 2015

I am not sure what to do with subgroup. Here are some examples:

xLevivirus subgroup I
plant rhabdoviruses subgroup B
Zelotes mayanus subgroup
Teuchophorus notabilis subgroup Meuffels & Grootaert 2004
Subgroup I Geminivirus
Sericania mimica subgroup Kobayashi & Fujioka 2008
Pipistrellus (Hypsugo) imbricatus subgroup

I will leave subgroup as is until I understand how to deal with it

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Everything except subgroups is covered in v3.1.10

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dimus commented May 14, 2015

Everything except subgroups is covered in v3.1.10

@dimus dimus closed this May 14, 2015

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