GBIF

[tpoisot]

I can generate a list of GBIF keys / taxon names, what is the best format for you to do the update?

[BenMerSci]

I got the time to generate them today and will upload them at the beginning of the week!

But I would be curious to see how you got them (if you already wrote a script for it), to compare the efficiency of my code (and how I could optimize it) compared to yours.

[tpoisot]

Here's my code:

using Pkg; Pkg.activate(".")
using GBIF
using Mangal
using JuliaDB, FileIO, CSV, IterableTables

backbone_size = count(MangalReferenceTaxon)

mangal_refs = backbone()
page = 0
while length(mangal_refs) < backbone_size
    global page += 1
    @info "page $(page)"
    next_page = backbone("page" => page)
    append!(mangal_refs, next_page)
end

mangal_refs

ids = NamedTuple[]

ids = NamedTuple[]
@progress for ref in mangal_refs
    try
        gbif_taxon = taxon(ref.name, strict=false)
        @info gbif_taxon.species
        if !ismissing(gbif_taxon.species)
            this_match = (
                id = ref.id, name = ref.name,
                confidence = gbif_taxon.confidence, match = gbif_taxon.match,
                status = gbif_taxon.status,
                gbif = gbif_taxon.species.second, gbifname = gbif_taxon.species.first
                )
            push!(ids, this_match)
        end
    catch
        @info "$(ref.name) has no species entry"
    end
end

table(ids) |> CSV.write("gbif.csv")

It's basically using the GBIF API to get the ID for anything with a match at the species level, and writes it to a CSV file. I'll attach the CSV file when it's done, it takes ~ 40 minutes to go through all taxa in Mangal.

[BenMerSci]

Is it in Julia?

[tpoisot]

Hell yeah

[tpoisot]

Here's the first 100 or so species -- note that GBIF has some updated names ( SYNONYM in status).

id	name	confidence	match	status	gbif	gbifname
1	Abutilon theophrasti	98	EXACT	ACCEPTED	3152614	Abutilon theophrasti
2	Acer negundo	98	EXACT	ACCEPTED	3189866	Acer negundo
3	Acer saccharinum	97	EXACT	ACCEPTED	3189837	Acer saccharinum
4	Achillea millefolium	98	EXACT	ACCEPTED	9221087	Achillea millefolium
7	Aesculus glabra	98	EXACT	ACCEPTED	3189806	Aesculus glabra
8	Aesculus hippocastanum	98	EXACT	ACCEPTED	3189815	Aesculus hippocastanum
9	Agastache nepetoides	98	EXACT	ACCEPTED	2926408	Agastache nepetoides
10	Agastache scrophulariaefolia	96	FUZZY	ACCEPTED	7307323	Agastache scrophulariaefolius
11	Agrimonia striata	98	EXACT	ACCEPTED	3001999	Agrimonia striata
12	Alisma plantago aquatica	92	FUZZY	ACCEPTED	2865100	Alisma plantago-aquatica
13	Amaranthus spinosus	98	EXACT	ACCEPTED	5384401	Amaranthus spinosus
14	Ambrosia trifida	98	EXACT	ACCEPTED	3110588	Ambrosia trifida
15	Amelanchier canadensis	97	EXACT	ACCEPTED	3023833	Amelanchier canadensis
16	Ammannia coccinea	97	EXACT	ACCEPTED	3188711	Ammannia coccinea
17	Amorpha canescens	98	EXACT	ACCEPTED	5357388	Amorpha canescens
18	Amorpha fruticosa	98	EXACT	ACCEPTED	5357407	Amorpha fruticosa
20	Anemonella thalictroides	97	EXACT	SYNONYM	3033114	Thalictrum thalictroides
21	Anethum graveolens	97	EXACT	ACCEPTED	3034646	Anethum graveolens
22	Antennaria plantaginifolia	98	EXACT	ACCEPTED	7459903	Antennaria plantaginifolia
23	Anthemis cotula	97	EXACT	ACCEPTED	8035698	Anthemis cotula
25	Apocynum androsaemifolium	98	EXACT	ACCEPTED	3169816	Apocynum androsaemifolium
26	Apocynum cannabinum	98	EXACT	ACCEPTED	3169790	Apocynum cannabinum
27	Aquilegia canadensis	97	EXACT	ACCEPTED	3033197	Aquilegia canadensis
31	Arctium minus	98	EXACT	ACCEPTED	5393103	Arctium minus
32	Arisaema triphyllum	97	EXACT	ACCEPTED	2867316	Arisaema triphyllum
33	Aristolochia tomentosa	98	EXACT	ACCEPTED	2874010	Aristolochia tomentosa
34	Aruncus sylvester	97	EXACT	ACCEPTED	8914718	Aruncus sylvester
37	Asclepias incarnata	97	EXACT	ACCEPTED	3170266	Asclepias incarnata
38	Asclepias purpurascens	97	EXACT	ACCEPTED	3170271	Asclepias purpurascens
39	Asclepias sullivantii	97	EXACT	ACCEPTED	3170265	Asclepias sullivantii
40	Asclepias syriaca	97	EXACT	ACCEPTED	3170247	Asclepias syriaca
41	Asclepias tuberosa	97	EXACT	ACCEPTED	3170305	Asclepias tuberosa
42	Asclepias verticillata	98	EXACT	ACCEPTED	3170235	Asclepias verticillata
44	Asparagus officinalis	98	EXACT	ACCEPTED	2768885	Asparagus officinalis
50	Aster paniculatus	97	EXACT	ACCEPTED	7930481	Aster paniculatus
52	Aster salicifolius	97	EXACT	ACCEPTED	7388527	Aster salicifolius
53	Aster turbinellus	97	EXACT	SYNONYM	3151488	Symphyotrichum turbinellum
54	Astragalus canadensis	98	EXACT	ACCEPTED	5345439	Astragalus canadensis
56	Baptisia bracteata	97	EXACT	ACCEPTED	2976054	Baptisia bracteata
57	Baptisia leucantha	98	EXACT	SYNONYM	2976072	Baptisia alba
58	Bidens aristosa	98	EXACT	ACCEPTED	5391901	Bidens aristosa
59	Bidens bipinnata	97	EXACT	ACCEPTED	5389402	Bidens bipinnata
60	Bidens connata	98	EXACT	ACCEPTED	5392083	Bidens connata
61	Bidens frondosa	97	EXACT	ACCEPTED	5392174	Bidens frondosa
62	Bidens laevis	98	EXACT	ACCEPTED	5391813	Bidens laevis
63	Blephilia ciliata	98	EXACT	ACCEPTED	2926502	Blephilia ciliata
64	Blephilia hirsuta	98	EXACT	ACCEPTED	2926501	Blephilia hirsuta
65	Boltonia asteroides	97	EXACT	ACCEPTED	5393593	Boltonia asteroides
72	Campanula americana	97	EXACT	ACCEPTED	5411082	Campanula americana

[tpoisot]

The code is also only return things that are identified to the species level -- it's possible to do them all but it's a bit more complicated and I don't want to do that on a weekend.

[BenMerSci]

Do you know what happened (or why they're not there) with some species that are not in your list? (for example : Arabis laevigata )

[tpoisot]

It's not in GBIF -- there genus Arabis is recognized, but this species is absent.

[BenMerSci]

Ok right. Had the same problem with get_gbifid (taxize) in R, the choice that I got were either only the genus, or some other Arabis sp. But then I realised that the accepted name of that species is now Boechera laevigata. I guess there are other species in the DB that have the same problem. Do you have an idea how we could screen them ?

[tpoisot]

If GBIF knows of the synonym, it will be in the table I'll send in ~ 25 minutes -- if not, there's no obvious way. A bunch of Salix species have the same issue (S. longifolia should be S. interior, see https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=520839#null). Maybe ITIS will have some information.

[tpoisot]

What I would do is

1. Get as many GBIF ids as possible
2. Replace the synonym names by the correct ones
3. When this is done, make a list of the problematic cases and see what we do

[BenMerSci]

Sounds good.

Also, maybe I would take your output of the GBIF ids and not mine, because for some reason (maybe there's something I didn't catch) but I wasn't able with the function get_gbifid to only match the exact species as the one I submitted.

Either I had to choose manually the one I wanted with the argument ''ask'' (and that would've been way too long considering there is more than 6000 species. Or I had to tell like get the first one of the list in GBIF and it wasnt always the good ID for the species I submitted (if you take for example : Arabis laevigata)

[tpoisot]

The gbif.txt file has info about 5000 taxa that are both resolved to the species level and have exact matches. This would leave 1700 taxa without a GBIF ID, but we can work through them later.

[tpoisot]

@SteveViss I would replace the names in mangal by the names in GBIF when the status is SYNONYM -- what do you think?

[SteveViss]

Yes @tpoisot, works for me.

[BenMerSci]

@tpoisot would you like me to work through the 1700 species or so that didn't have a gbif ID to check their names to see if there is a more up to date name? ( and retrieve the associated taxonomic ids)

[tpoisot]

I'll do that later this week - it's not really difficult but there are a few tricks.

Get Outlook for Androidhttps://aka.ms/ghei36

---

From: BenMerSci notifications@github.com Sent: Monday, April 8, 2019 4:11:34 PM To: mangal-wg/mangal-api Cc: Poisot Timothée; Mention Subject: Re: [mangal-wg/mangal-api] GBIF (#43)

@tpoisothttps://github.com/tpoisot would you like me to work through the 1700 species or so that didn't have a gbif ID to check their names to see if there is a more up to date name? ( and retrieve the associated taxonomic ids)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/mangal-wg/mangal-api/issues/43#issuecomment-480988530, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AAjXAb3sqJTtDiL_qI2TPR0f5iyVhEdXks5ve6J2gaJpZM4cf7ih.

[BenMerSci]

If possible, i'd really like to know how, because I didn't find any way to find the accepted synonym and up to date name of a scientific name through R (by using existant function from packages).

[SteveViss]

The solution is not trivial in R but you have some clues/tips here: https://gist.github.com/sckott/c1e2cb547d9f22bd314da50fe9c7b503

[tpoisot]

GBIF codes are pointing to the latest synonym, so we can (afaic) keep the old name and get ids first, then resolve.

Get Outlook for Androidhttps://aka.ms/ghei36

---

From: Steve Vissault notifications@github.com Sent: Monday, April 8, 2019 5:12:53 PM To: mangal-wg/mangal-api Cc: Poisot Timothée; Mention Subject: Re: [mangal-wg/mangal-api] GBIF (#43)

The solution is not trivial in R but you have some clues/tips here: https://gist.github.com/sckott/c1e2cb547d9f22bd314da50fe9c7b503

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/mangal-wg/mangal-api/issues/43#issuecomment-481010178, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AAjXAZas8RuDt9ofyV6q-DRbFhOMqDkxks5ve7DVgaJpZM4cf7ih.

[tpoisot]

The issue is also that not all nodes are species, so we also have to figure out the taxonomic rank.

Get Outlook for Androidhttps://aka.ms/ghei36

---

From: Poisot Timothée Sent: Monday, April 8, 2019 5:14:18 PM To: mangal-wg/mangal-api; mangal-wg/mangal-api Cc: Mention Subject: Re: [mangal-wg/mangal-api] GBIF (#43)

GBIF codes are pointing to the latest synonym, so we can (afaic) keep the old name and get ids first, then resolve.

Get Outlook for Androidhttps://aka.ms/ghei36

---

From: Steve Vissault notifications@github.com Sent: Monday, April 8, 2019 5:12:53 PM To: mangal-wg/mangal-api Cc: Poisot Timothée; Mention Subject: Re: [mangal-wg/mangal-api] GBIF (#43)

The solution is not trivial in R but you have some clues/tips here: https://gist.github.com/sckott/c1e2cb547d9f22bd314da50fe9c7b503

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/mangal-wg/mangal-api/issues/43#issuecomment-481010178, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AAjXAZas8RuDt9ofyV6q-DRbFhOMqDkxks5ve7DVgaJpZM4cf7ih.

[SteveViss]

Note (Thanks to @BenMerSci ): GBIF accepted names is unconsistent with COL (http://www.catalogueoflife.org/). We compared the original name requested with the accept name provided by both services. GBIF appears to be more accurate and reliable. Thus, we choose to keep the accepted names offer by GBIF and store them as final taxonomic names (with GBIF taxa rank) in Mangal.

id	original_name	gbif_name	gbif_id	status_gbif	col_id	col_name	rank_col	status_col
23	Anthemis cotula	Anthemis cotula	8035698	ACCEPTED	1788793824d569d6f13704a26129ea80	Eclipta alba	species	accepted name
34	Aruncus sylvester	Aruncus sylvester	8914718	ACCEPTED	a0ac0139581fb995b67c31327bb88c25	Aruncus dioicus	species	accepted name
40	Asclepias syriaca	Asclepias syriaca	3170247	ACCEPTED	3d79fe6331601bc51289d80ab8f3ac57	Asclepias curassavica	species	accepted name
41	Asclepias tuberosa	Asclepias tuberosa	3170305	ACCEPTED	8d1f5fcefa20c20e9cb74a913f0e7fad	Leptadenia reticulata	species	accepted name
50	Aster paniculatus	Aster paniculatus	7930481	ACCEPTED	c80dd6d170730484f466451ee91afe53	Symphyotrichum undulatum	species	accepted name
52	Aster salicifolius	Aster salicifolius	7388527	ACCEPTED	91eb156c80cd17a8e044bbdbc716290e	Symphyotrichum boreale	species	accepted name
59	Bidens bipinnata	Bidens bipinnata	5389402	ACCEPTED	d448bfb551adadec97722ec64c13c066	Cosmos bipinnatus	species	accepted name
65	Boltonia asteroides	Boltonia asteroides	5393593	ACCEPTED	2f3f1cd0f366ac84a7ac8c38758f50e3	Boltonia diffusa	species	accepted name
79	Caulophyllum thalictroides	Caulophyllum thalictroides	3033920	ACCEPTED	2be34cf24869f18508958a0d1b14ef7a	Caulophyllum robustum	species	accepted name
82	Cephalanthus occidentalis	Cephalanthus occidentalis	2923947	ACCEPTED	1ea31e5987271b46bb69da8df0d1c691	Cephalanthus tetrandra	species	accepted name
88	Cicuta maculata	Cicuta maculata	5371867	ACCEPTED	b848aad3ce130d5d7021a24e7689c5d4	Cicuta douglasii	species	accepted name
115	Cynoglossum officinale	Cynoglossum officinale	2925815	ACCEPTED	8db381ee702702439bc8f3a8d5f41b3e	Cynoglossum dioscoridis	species	accepted name
128	Desmodium paniculatum	Desmodium paniculatum	2967543	ACCEPTED	d31f03fe295c837d97a3db136e3dc1f3	Desmodium glabellum	species	accepted name
149	Eupatorium coelestinum	Eupatorium coelestinum	7400732	ACCEPTED	5529ee5bab0282ae2bfcfb2bfb93d629	Conoclinium coelestinum	species	accepted name
151	Eupatorium purpureum	Eupatorium purpureum	8311325	ACCEPTED	e229c74162247ce048ffb49104ffa63e	Eutrochium purpureum	species	accepted name
172	Geum canadense	Geum canadense	5369800	ACCEPTED	c31b9e9ae3ab2acc46a5323ee3e4d09d	Geum aleppicum	species	accepted name
184	Helianthus divaricatus	Helianthus divaricatus	3119249	ACCEPTED	0509ab08a046da8b30ec2ed2b7fbb7a8	Helianthus microcephalus	species	accepted name
239	Lobelia spicata	Lobelia spicata	5408750	ACCEPTED	cbf8c3a2f0aee9da373a7d933295dae9	Lobelia fenestralis	species	accepted name
245	Lythrum alatum	Lythrum alatum	3188732	ACCEPTED	67a1dcf6978b71f1b1451c22b7f5747b	Lythrum maritimum	species	accepted name
265	Oenothera biennis	Oenothera biennis	3188924	ACCEPTED	1a809dbfeb49e2567256a9553797e615	Oenothera laciniata	species	accepted name
274	Panicum virgatum	Panicum virgatum	2705081	ACCEPTED	15acf3b27ab6e5af6fedabc2de41d9c0	Panicum flexuosum	species	accepted name
276	Passiflora lutea	Passiflora lutea	2874220	ACCEPTED	638dc908c790a433b7e3b94a77d1abce	Passiflora subpeltata	species	accepted name
287	Physalis lanceolata	Physalis lanceolata	5341790	ACCEPTED	c84f684300d0a6470640817982b39b0b	Physalis viscosa	species	accepted name
307	Pontederia cordata	Pontederia cordata	2766030	ACCEPTED	08e190d523f6aa8d62a801e5d4823407	Monochoria vaginalis	species	accepted name
341	Rubus occidentalis	Rubus occidentalis	2991466	ACCEPTED	719ce345201803e46f48c31d890e3584	Rubus mesogaeus	species	accepted name
368	Senecio aureus	Senecio aureus	8299464	ACCEPTED	0644eb0bf5abe32da72ed4fd04cdd92c	Packera aurea	species	accepted name
370	Sicyos angulatus	Sicyos angulatus	2874655	ACCEPTED	0cc91dab40ac7c99bf5ac7f751b25f00	Sicyos australis	species	accepted name
375	Silphium laciniatum	Silphium laciniatum	3092583	ACCEPTED	90ad6948a370679caefbb53563716719	Silphium compositum	species	accepted name
377	Silphium terebinthinaceum	Silphium terebinthinaceum	7475866	ACCEPTED	90ad6948a370679caefbb53563716719	Silphium compositum	species	accepted name
384	Smilax herbacea	Smilax herbacea	5295311	ACCEPTED	00b98f015fb9f7590682e90d021ad6c7	Smilax anceps	species	accepted name
394	Solidago serotina	Solidago serotina	8043913	ACCEPTED	e0f03a65926fa728d85c944e3570f3e9	Solidago missouriensis	species	accepted name
404	Stellaria longifolia	Stellaria longifolia	5384658	ACCEPTED	aad148d66034ff71d5120f42cb0659a2	Stellaria graminea	species	accepted name
405	Stellaria media	Stellaria media	5384604	ACCEPTED	9a6ecdd3a1d29d5f002addac9f570106	Stellaria palustris	species	accepted name
407	Strophostyles helvola	Strophostyles helvola	3912996	ACCEPTED	b51cd2af3504637a6cf8a872d0a432c2	Strophostyles helvula	species	accepted name
439	Verbesina helianthoides	Verbesina helianthoides	7792715	ACCEPTED	23256eb46e64b76938567e779bebafdf	Dimerostemma grisebachii	species	accepted name
452	Vitis cordifolia	Vitis cordifolia	7974629	ACCEPTED	64a2fd3f5039c634a4b2efec6955d27c	Vitis vulpina	species	accepted name
453	Vitis vulpina	Vitis vulpina	5372401	ACCEPTED	ae5711c8860b64c05a38046e21410da9	Vitis labrusca	species	accepted name
596	Cerceris clypeata	Cerceris clypeata	1338923	ACCEPTED	86e579f0e0f842be00e3537714159042	Cerceris prominens	species	accepted name
685	Helophilus latifrons	Helophilus latifrons	5071343	ACCEPTED	e5b2cc8f53e9634b6ba02d3ea6ba1477	Helophilus hochstetteri	species	accepted name
734	Tachysphex terminatus	Tachysphex terminatus	8288100	ACCEPTED	3179ef524b47410a304ef132f401a43e	Tachysphex similis	species	accepted name
838	Bombylius pulchellus	Bombylius pulchellus	5092903	ACCEPTED	dc77a0abc78a9e52a1baa4d2a2b41c7a	Bombylius dives	species	accepted name
990	Cerceris rufinoda	Cerceris rufinoda	8370074	ACCEPTED	8fbd1ca70c9c01803a7778d1c9770d6c	Cerceris crucis	species	accepted name
1116	Tachytes distinctus	Tachytes distinctus	7412329	ACCEPTED	2db7b7213af3085204ba6f7a794e9b21	Tachytes auricomans	species	accepted name
1252	Tachysphex tarsatus	Tachysphex tarsatus	7558944	ACCEPTED	a6b869047ad04fe9727961b3efe2fd97	Tachysphex pechumani	species	accepted name
1338	Eurytoma diastrophi	Eurytoma diastrophi	5045149	ACCEPTED	a779b67906b60e8a2e298574f9709292	Eurytoma mayri	species	accepted name
1341	Agrilus egenus	Agrilus egenus	6004122	ACCEPTED	bfaea82c7895ed6392e3f1fbef298e3f	Agrilus cuprescens	species	accepted name
1499	Cerastium alpinum	Cerastium alpinum	3085450	ACCEPTED	d5f840b6667189d5e1aebfb21587f266	Cerastium glomeratum	species	accepted name
1516	Salix arctica	Salix arctica	5372665	ACCEPTED	34df40462b734c74d824d0b39db5d5c5	Salix arctophila	species	accepted name
1517	Saxifraga cernua	Saxifraga cernua	3032869	ACCEPTED	c7846695cb89e2f776d03384e9597754	Saxifraga granulata	species	accepted name
1542	Tipula arctica	Tipula arctica	1505093	ACCEPTED	3a073c5dbfe808c9a50b7a7f6acbb541	Tipula sinarctica	species	accepted name
1766	Miconia pusilliflora	Miconia pusilliflora	3869773	ACCEPTED	ae250a02d0b5987c0356f27b8e83b141	Miconia affinis	species	accepted name
1783	Miconia theaezans	Miconia theaezans	3188576	ACCEPTED	a5172d9044010d37689e0b4d67b21a2a	Miconia theizans	species	accepted name
1785	Nectandra membranacea	Nectandra membranacea	5371736	ACCEPTED	c2a849b4d291069604e62bce25a98c8b	Nectandra megapotamica	species	accepted name
1816	Miconia discolor	Miconia discolor	3867661	ACCEPTED	adde6f380bbbf493cca53f28019a45b9	Miconia punctata	species	accepted name
1858	Inga marginata	Inga marginata	7574428	ACCEPTED	16dc8ec9058137fe6f946212f15ddc0c	Inga semialata	species	accepted name
1868	Piper aduncum	Piper aduncum	3086337	ACCEPTED	0c45507e189c8e314f23f43707101bcf	Piper hispidum	species	accepted name
1903	Solanum americanum	Solanum americanum	2930222	ACCEPTED	756ccbdfdd26883b213c087fff0b90fb	Solanum ptychanthum	species	accepted name
1951	Strychnos brasiliensis	Strychnos brasiliensis	7289390	ACCEPTED	deb245cee14cf0d134d43420bf5ff2d7	Strychnos parvifolia	species	accepted name
2060	Dolichopus plumipes	Dolichopus plumipes	8419922	ACCEPTED	6ebf2f34a413d5ce8e88f54215b03904	Tachytrechus ammobates	species	accepted name
2289	Cerastium arvense	Cerastium arvense	3085433	ACCEPTED	906a03cd9aa3a5036addaf7d8ec7393a	Cerastium orithales	species	accepted name
2329	Loasa heterophylla	Loasa heterophylla	8383700	ACCEPTED	225455aded08ad8cdc4e0b083f66f677	Loasa tricolor	species	accepted name
2342	Acaena pinnatifida	Acaena pinnatifida	5370645	ACCEPTED	db38b88b89a97981d2d1d2749fbd8af8	Acaena trifida	species	accepted name
2471	Chaetanthera apiculata	Chaetanthera apiculata	8836450	ACCEPTED	1f80b966fb87df7bfb03608a64a3f3a9	Oriastrum apiculatum	species	accepted name
2473	Chaetanthera lycopodioides	Chaetanthera lycopodioides	5402560	ACCEPTED	363a26718a6456bdd34f71440850a1d9	Oriastrum lycopodioides	species	accepted name
2655	Cordia sebestena	Cordia sebestena	5341289	ACCEPTED	7ab4026f6dca4c977509408251784b79	Cordia subcordata	species	accepted name
2693	Solanum torvum	Solanum torvum	2932389	ACCEPTED	8dff60dfb5cde89b9490f039414dbf88	Solanum stramonifolium	species	accepted name
2697	Merremia umbellata	Merremia umbellata	8819344	ACCEPTED	712e1913dfc8bd46ff10283e3d350dc6	Camonea umbellata	species	accepted name
2707	Euphorbia heterophylla	Euphorbia heterophylla	3064495	ACCEPTED	817c27c93428c9ae46b20b7795881caa	Euphorbia terracina	species	accepted name
2740	Amphiprion akallopisos	Amphiprion akallopisos	5212090	ACCEPTED	4118e4f7397e1684eb200cb3c7ff07f7	Amphiprion sandaracinos	species	accepted name
2784	Geoffroea spinosa	Geoffroea spinosa	2966693	ACCEPTED	191773a3458c0cc212403396554b98a4	Geoffroea decorticans	species	accepted name
2790	Mentzelia aspera	Mentzelia aspera	5331416	ACCEPTED	9f83b85d11b645c4761ec77ce2642f7a	Mentzelia hispida	species	accepted name
2801	Sida rhombifolia	Sida rhombifolia	5406735	ACCEPTED	eb274eb20557cde348cffe4aba5bc76d	Sida alnifolia	species	accepted name
2805	Inga edulis	Inga edulis	5357677	ACCEPTED	46443e926bf39e1b440e5ef2424caacf	Inga feuilleei	species	accepted name
2827	Physalis pubescens	Physalis pubescens	5341819	ACCEPTED	855697b49699c4775e1640edd1e7bc53	Physalis lagascae	species	accepted name
3076	Lonicera alpigena	Lonicera alpigena	6369729	ACCEPTED	c725b0c1ec80391d72bed06a3b4399a6	Lonicera microphylla	species	accepted name
3084	Pedicularis resupinata	Pedicularis resupinata	8140157	ACCEPTED	bc6b4b02c865ea37c4e3666890862dad	Pedicularis lanceolata	species	accepted name
3094	Libanotis coreana	Libanotis coreana	5540555	ACCEPTED	809eb052859569528d8fe3c48ee91e23	Seseli coreanum	species	accepted name
3121	Ribes maximowiczianum	Ribes maximowiczianum	4927325	ACCEPTED	58a6f93e68e610ff8fb49c5e735c71da	Ribes komarovii	species	accepted name
3123	Hydrangea paniculata	Hydrangea paniculata	2985995	ACCEPTED	a53f200acde69f10222887d6e7cb9d49	Hydrangea arborescens	species	accepted name
3198	Ossaea micrantha	Ossaea micrantha	3862996	ACCEPTED	622bcb41d0f16647eaf2e64cb458b6fc	Miconia neomicrantha	species	accepted name
3204	Zanthoxylum culantrillo	Zanthoxylum culantrillo	9099416	ACCEPTED	9e9a41f172b98c93411d683c246c712a	Zanthoxylum fagara culantrillo	infraspecies	accepted name
3238	Phoebe mexicana	Phoebe mexicana	1113004	ACCEPTED	337ad018789c0fc442e8b285dcd6362a	Cinnamomum triplinerve	species	accepted name
3241	Piper auritum	Piper auritum	3086352	ACCEPTED	ba5cf915a4a7d2f295d7fc76ba88ad13	Piper dilatatum	species	accepted name
3275	Solanum umbellatum	Solanum umbellatum	2929008	ACCEPTED	e00068fb978869c5091caacc11a4aa80	Lycianthes pauciflora	species	accepted name
3543	Microtus arvalis	Microtus arvalis	2438606	ACCEPTED	c316d43b9cbe48bea99f1d1a1f0c3f3d	Microtus mongolicus	species	accepted name
3649	Sciurus vulgaris	Sciurus vulgaris	8211070	ACCEPTED	49d7a71659f9bb7608085738bd0984e6	Sciurus vulgaris cinerea	infraspecies	accepted name
3756	Leontodon taraxacoides	Leontodon taraxacoides	7997328	ACCEPTED	51ba1e2da7b10df7266440102514dc98	Leontodon saxatilis saxatilis	infraspecies	accepted name
3762	Sonchus tenerrimus	Sonchus tenerrimus	3105768	ACCEPTED	48d2a7846586eb95b9aaf93cf320570a	Sonchus oleraceus	species	accepted name
4128	Daphnia pulex	Daphnia pulex	2234840	ACCEPTED	d5ec41e2cfe29e552a40310c6c4a2d36	Daphnia parapulex	species	accepted name
4157	Gymnodinium palustre	Gymnodinium palustre	8172141	ACCEPTED	cd3f60f84cdbf575303b2423e897aacd	Gymnodinium zachariasi	species	accepted name
4173	Salmo trutta	Salmo trutta	8215487	ACCEPTED	3d9e5032ec6a0c4b846544e2db56fa0a	Salmo tigridis	species	accepted name
4201	Rhizosolenia eriensis	Rhizosolenia eriensis	9537778	ACCEPTED	27f91d8f55c03b6c9db558b9ef801d46	Urosolenia eriensis	species	accepted name
4255	Coregonus clupeaformis	Coregonus clupeaformis	2351119	ACCEPTED	f59b83d471ad480c2406e3b60f2422a3	Coregonus huntsmani	species	accepted name
4525	Balanus eburneus	Balanus eburneus	2115699	ACCEPTED	952472954f45e51d249d65fd0f437cea	Amphibalanus eburneus	species	accepted name
4655	Gambusia affinis	Gambusia affinis	2350580	ACCEPTED	25a7319f62791093ee453c590a48923f	Gambusia marshi	species	accepted name
4665	Carcharhinus leucas	Carcharhinus leucas	2418036	ACCEPTED	1636fc18b4ff37be394d4a9abc76b1ba	Carcharhinus amboinensis	species	accepted name
4751	Sphaerium tasmanicum	Sphaerium tasmanicum	5794108	ACCEPTED	3047f9102ea94c8135150e0b94fc44a0	Musculium tasmanicum	species	accepted name
4881	Squalus acanthias	Squalus acanthias	5216368	ACCEPTED	81ac8fff6e416a1ac6ae7ce88e83f702	Squalus suckleyi	species	accepted name
4907	Crassostrea angulata	Crassostrea angulata	2286078	ACCEPTED	0db6d26acc8f368a046f1a9fd6b63d76	Magallana angulata	species	accepted name
4922	Conger conger	Conger conger	2403490	ACCEPTED	6ff354642749bc7f02542a611a030491	Conger wilsoni	species	accepted name
4940	Somniosus microcephalus	Somniosus microcephalus	2421162	ACCEPTED	e78bdad5395a4d280829c7dde2d26565	Somniosus pacificus	species	accepted name
5048	Carduus pycnocephalus	Carduus pycnocephalus	3114667	ACCEPTED	e809ca9a25c6eda109f9580e30221c1d	Carduus cephalanthus	species	accepted name
5125	Helenium puberulum	Helenium puberulum	5401829	ACCEPTED	bca86a956e44b0060a92947e157a23fe	Helenium vernale	species	accepted name
5135	Melilotus officinalis	Melilotus officinalis	2971024	ACCEPTED	13e2ed8b03e46e59fb95352a01f060d6	Melilotus suaveolens	species	accepted name
5232	Rubus ursinus	Rubus ursinus	2990646	ACCEPTED	bf55b3080755f39116f502176604fe45	Rubus spectabilis	species	accepted name
5377	Auchenipterus nuchalis	Auchenipterus nuchalis	2344578	ACCEPTED	cef2c648cca106890b8891a86deec699	Epapterus dispilurus	species	accepted name
5383	Serrasalmus spilopleura	Serrasalmus spilopleura	2354120	ACCEPTED	f61491339d3d85a4ee54ca0ea0be5341	Serrasalmus maculatus	species	accepted name
5397	Salminus brasiliensis	Salminus brasiliensis	2354769	ACCEPTED	81e20e5a894d266afa08f35f94860b31	Salminus franciscanus	species	accepted name
5408	Astyanax fasciatus	Astyanax fasciatus	5204200	ACCEPTED	eb928f07fb7dceb0815e51a5108e3928	Astyanax scabripinnis	species	accepted name
5497	Lepus americanus	Lepus americanus	2436794	ACCEPTED	20dc5942fef7f3aac468c65afb14815f	Lepus americanus cascadensis	infraspecies	accepted name
5604	Barbus paludinosus	Barbus paludinosus	8972660	ACCEPTED	34dc51e16fbd65f21b32d0709a54d6b7	Enteromius paludinosus	species	accepted name
5628	Pseudotropheus elongatus	Pseudotropheus elongatus	2373066	ACCEPTED	a6a14662b65dcf4be52092df2a948010	Pseudotropheus cyaneus	species	accepted name
5639	Labidochromis vellicans	Labidochromis vellicans	2371647	ACCEPTED	2b9d57047f326f8616cfe64329d74d79	Labidochromis maculicauda	species	accepted name
5668	Labeo mesops	Labeo mesops	5206085	ACCEPTED	28c0f64f1048db94234aa1416d7ea48a	Labeo rosae	species	accepted name
5878	Acanthopagrus berda	Acanthopagrus berda	2392290	ACCEPTED	e3e9791df568d71f2d97fb2f16a58b19	Acanthopagrus pacificus	species	accepted name
5887	Gerres filamentosus	Gerres filamentosus	2369436	ACCEPTED	3e1ac1b509404393dd86aec8227e183d	Gerres macracanthus	species	accepted name
5891	Hephaestus tulliensis	Hephaestus tulliensis	2374620	ACCEPTED	6be118ba4df8b789cc45ee41f415150d	Hephaestus fuliginosus	species	accepted name
5895	Leiognathus equulus	Leiognathus equulus	5211415	ACCEPTED	8d8937ad495921f431b63675bf0ab53a	Karalla dussumieri	species	accepted name
5897	Microphis brachyurus	Microphis brachyurus	5712324	ACCEPTED	fbe64cb7a9af02560d2ba4eb19101531	Microphis millepunctatus	species	accepted name
5924	Euceraphis betulae	Euceraphis betulae	9816855	ACCEPTED	4b5d128b49888a76e1d0ebfe510eae6b	Euceraphis punctipennis	species	accepted name
6243	Heliconia bihai	Heliconia bihai	7865486	ACCEPTED	d159d2661f81c03466cd761ed546efef	Strelitzia reginae	species	accepted name
6260	Cetraria delisei	Cetraria delisei	8843098	ACCEPTED	2d1e5ed85183a0dc90f31ace5cdf6654	Cetrariella delisei	species	accepted name
6279	Sciurus niger	Sciurus niger	5219683	ACCEPTED	ba589d22a02c9409aa33c415fccf4af9	Sciurus niger avicennia	infraspecies	accepted name
6351	Mormyrus longirostris	Mormyrus longirostris	2402714	ACCEPTED	28bc2da71194bf5aad95415a4428ed47	Mormyrus caschive	species	accepted name
6390	Asellus bivittatus	Asellus bivittatus	8759895	ACCEPTED	6b5494429d259dd571beed50c6fa9c7c	Caecidotea brevicauda bivittatus	infraspecies	accepted name
6455	Eiseniella tetraedra	Eiseniella tetraedra	2307762	ACCEPTED	e4dfbffd2d0ceca875d4613122151869	Eiseniella tetra�dra	species	accepted name
6669	Torymus auratus	Torymus auratus	1371917	ACCEPTED	ba181d6bad4f6f6a5d6a5a31758427db	Torymus flavipes	species	accepted name
6822	Achnanthes minutissima	Achnanthes minutissima	7934456	ACCEPTED	6dc7aff867748a92cccf4c0b44a6f7ef	Achnanthidium minutissimum	species	accepted name
6892	Navicula placentula	Navicula placentula	5269322	ACCEPTED	f8d14192054789eb965bc130d3ceffaf	Placoneis placentula	species	accepted name
6914	Navicula mutica	Navicula mutica	7524494	ACCEPTED	afabc906aa7d98856726929b5fb3f393	Luticola mutica	species	accepted name
6915	Navicula dicephala	Navicula dicephala	7641549	ACCEPTED	36b99870e24443b83c6b48d4972785e1	Placoneis dicephala	species	accepted name
6955	Gomphonema intricatum	Gomphonema intricatum	7369068	ACCEPTED	141e28e7b21310d5ca8a1a79ad6459d2	Gomphonema vibrio intricatum	infraspecies	accepted name
6956	Diatoma elongatum	Diatoma elongatum	9590269	ACCEPTED	95b1f90741ad2d7be9c5b8a714b8e834	Diatoma tenue elongatum	infraspecies	accepted name
7018	Empoasca fabae	Empoasca fabae	8061113	ACCEPTED	6979387922e4e06fd9e848404c58f096	Empoasca alsiosa	species	accepted name
7109	Tachysphex unicolor	Tachysphex unicolor	4495090	ACCEPTED	6caab10d9dca86824935aa540c87ab10	Tachysphex nitidus	species	accepted name
7219	Mimusops erythroxylon	Mimusops erythroxylon	2883726	ACCEPTED	28c8210292ca1d80225c6635c5170d38	Mimusops elengi	species	accepted name
7260	Casearia coriacea	Casearia coriacea	7916423	ACCEPTED	b5f3f4d12070463a289ea5b0f81a1210	Casearia thwaitesii	species	accepted name
7301	Rubus alceifolius	Rubus alceifolius	2997267	ACCEPTED	f023c78b2f11f6192d76bd40c2c01b48	Rubus rolfei	species	accepted name
7361	Paraserianthes falcataria	Paraserianthes falcataria	8232636	ACCEPTED	25d04191a1364cbf77b599da7198c1c1	Falcataria moluccana	species	accepted name
7401	Ficus trichocarpa	Ficus trichocarpa	5572273	ACCEPTED	703be2f3b1c653d45171ff831a87e859	Ficus racemosa	species	accepted name
7709	Echium vulgare	Echium vulgare	2925892	ACCEPTED	33a04156dbb79562e2c2c878dd8f0fce	Echium rauwolfii	species	accepted name
7744	Hieracium praealtum	Hieracium praealtum	8098407	ACCEPTED	a2f0679c5a798fde37460afb1ee8dfa8	Pilosella praealta	species	accepted name
7763	Berlinia bracteosa	Berlinia bracteosa	2971336	ACCEPTED	7c900fbb011749289de21ecc5dafc0a5	Berlinia occidentalis	species	accepted name
7790	Lespedeza bicolor	Lespedeza bicolor	2955759	ACCEPTED	3c5ee4ed6d86e2177a5a091dfcdccaad	Lespedeza floribunda	species	accepted name
7799	Spiraea japonica	Spiraea japonica	8170635	ACCEPTED	39196cf5f1f597895b473b26ba1df611	Spiraea thunbergii	species	accepted name
7813	Aster scaber	Aster scaber	5404913	ACCEPTED	c80dd6d170730484f466451ee91afe53	Symphyotrichum undulatum	species	accepted name
7827	Inula salicina	Inula salicina	3148413	ACCEPTED	4ce7ac4ec20121378ea83529cb673cc5	Inula acuminata	species	accepted name
7836	Dianthus superbus	Dianthus superbus	6363496	ACCEPTED	68f58e4c63df157c03b33c587c49b2a5	Dianthus broteri	species	accepted name
7912	Paragus quadrifasciatus	Paragus quadrifasciatus	1535807	ACCEPTED	85e7a364179bf96c99161ad666368fac	Spilomyia sayi	species	accepted name
8007	Trachys saundersi	Trachys saundersi	6131833	ACCEPTED	83bec420f66562913f1e727f0c1f6610	Habroloma saundersi	species	accepted name
8054	Rallus crepitans	Rallus crepitans	7751637	ACCEPTED	66e4377b29129bd9274dbae9257bc5d5	Rallus longirostris crepitans	infraspecies	accepted name
8064	Salix caprea	Salix caprea	5372952	ACCEPTED	fb2eff1f9c9b49d58be745cdf2ddb0b5	Salix lanata	species	accepted name
8072	Salix fragilis	Salix fragilis	5372829	ACCEPTED	be0aba4aeeadd9f6c8f4ebe2741599d0	Salix rubens	species	accepted name
8087	Salix retusa	Salix retusa	8119241	ACCEPTED	72660253ca6e4522875daec39a5b7410	Salix uva-ursi	species	accepted name
8104	Salix repens	Salix repens	9148812	ACCEPTED	967dbe7a667bb6a0a53b359188e97432	Salix argyrocarpa	species	accepted name
8120	Salix myrtilloides	Salix myrtilloides	7482782	ACCEPTED	349922c14340ea134395192b9a202fb4	Salix fuscescens	species	accepted name
8126	Salix herbacea	Salix herbacea	5373083	ACCEPTED	7a8cc97893be882cb6c029469d692945	Salix polaris	species	accepted name
8142	Salix pentandra	Salix pentandra	5372647	ACCEPTED	94e126020a177f11fdb7c0c489a71c74	Salix hexandra	species	accepted name
8165	Salix rubens	Salix rubens	5372512	ACCEPTED	750a240440786bd94ad45cc1ea0c6b8b	Salix silesiaca	species	accepted name
8169	Salix rosmarinifolia	Salix rosmarinifolia	7104059	ACCEPTED	349922c14340ea134395192b9a202fb4	Salix fuscescens	species	accepted name
8179	Salix bicolor	Salix bicolor	5372945	ACCEPTED	051212f71522a8a4bbf32c91a28c08a4	Salix starkeana	species	accepted name
8297	Pimpinella major	Pimpinella major	5371874	ACCEPTED	b34cbecfb7f964d914c79ec2ebc9bd0d	Pimpinella saxifraga	species	accepted name
8302	Leontodon autumnalis	Leontodon autumnalis	8058115	ACCEPTED	36917f67553275a2bbcb6b9f76110324	Scorzoneroides autumnalis autumnalis	infraspecies	accepted name
8303	Leontodon hispidus	Leontodon hispidus	3137498	ACCEPTED	14f5c5b4c42573bd69c47e9a9098cacd	Leontodon crispus	species	accepted name
8328	Alopecurus pratensis	Alopecurus pratensis	5290081	ACCEPTED	0ff5491ccd0746c6818d4e96c559de17	Alopecurus arundinaceus	species	accepted name
8333	Bromus hordeaceus	Bromus hordeaceus	2703777	ACCEPTED	1344d48c2f73160ddeada1c1dfd58455	Bromus secalinus	species	accepted name
8360	Rhyparochromus pini	Rhyparochromus pini	5758859	ACCEPTED	b6efcfec85177968bedd3dfefe64508f	Rhyparochromus pini intermedius	infraspecies	accepted name
8494	Amara nitida	Amara nitida	8396839	ACCEPTED	00e47d56cb22f3f862d9b3666d52d3b1	Amara sinuosa	species	accepted name
8495	Amara ovata	Amara ovata	8563753	ACCEPTED	d872706e42cf1d1d6567f3c7d1a80021	Amara littorea	species	accepted name
8514	Harpalus latus	Harpalus latus	5755339	ACCEPTED	5375fd73d184335a2a5b08198cfb73df	Harpalus tardus	species	accepted name
8516	Leistus ferrugineus	Leistus ferrugineus	4473860	ACCEPTED	24d04aef635b4643fa9574be5a636485	Leistus ferruginosus	species	accepted name
8524	Ophonus laticollis	Ophonus laticollis	4475157	ACCEPTED	664fdafb054d11fecde19bb98cd396cd	Ophonus puncticollis	species	accepted name
8531	Pterostichus strenuus	Pterostichus strenuus	7508714	ACCEPTED	f433a9f2c6b5ac919874bbe7165b36b9	Pterostichus diligens	species	accepted name
8573	Atheta elongatula	Atheta elongatula	6097477	ACCEPTED	7389ba21beed9de0816b5f814ee73581	Atheta pseudoelongatula	species	accepted name
8576	Atheta triangulum	Atheta triangulum	6097459	ACCEPTED	e9a5f1d7fd99d8cd9021efea78f2475a	Atheta pseudotriangulum	species	accepted name
8646	Empoasca decipiens	Empoasca decipiens	5985391	ACCEPTED	339a2055ab13015d774d1b18723f1b08	Empoasca punjabensis	species	accepted name
8649	Eupteryx notata	Eupteryx notata	5984871	ACCEPTED	7238179edff374b75d0ee40f8d36ac6a	Eupteryx vittata	species	accepted name
8670	Empoasca pteridis	Empoasca pteridis	8632285	ACCEPTED	a79569ebc55d0647b3c7c4b3a1b60adc	Empoasca affinis	species	accepted name
8853	Oxypoda brachyptera	Oxypoda brachyptera	6097518	ACCEPTED	cb9e9b5812b09e3eace7520be7d40a79	Oxypoda parvipennis	species	accepted name
8869	Lithobius microps	Lithobius microps	2229915	ACCEPTED	c51b4d4953bcc376a82a1ade512ea104	Lithobius lapidicola	species	accepted name
8877	Lithobius piceus	Lithobius piceus	2230181	ACCEPTED	4b020dfdd7bb493ebcc50b4ea12f0964	Guambius oedipes	species	accepted name
8884	Harpalus rufipes	Harpalus rufipes	9251010	ACCEPTED	0034833298e56a7a559add7ad5ed8696	Ophonus stictus	species	accepted name
8969	Chorthippus apricarius	Chorthippus apricarius	1708601	ACCEPTED	136685c3a3ee5a7601cb7401e8241c78	Chorthippus apricarius asiaticus	infraspecies	accepted name
8970	Chorthippus biguttulus	Chorthippus biguttulus	1708251	ACCEPTED	e40701bc54d3c5322000a5d4af4cf140	Chorthippus yersini	species	accepted name

[SteveViss]

Reassigned to #47