Documentation for S1000 corpus annotation

Original Curator Guidelines for S800 corpus

The annotation guidelines as described in the original publication of the S800 corpus

The guidelines to curators were to annotate all substrings, which can meaningfully be identified as referring to a taxon. While the main focus was on annotating species mentions, strings referring to any taxonomic level, (e.g.kingdoms, orders, genera, strains) were also considered. The data for upper taxonomic level annotations were never officially released.

The main guidelines were:

All document substrings must be evaluated and all mentions including repetitions should be listed in the order of appearance in the text.
The annotated name types among others should include: Linnaean binomials, common names, strain names, author defined acronyms.
For each annotated string, curators must record the name as it appeared in text and report the corresponding NCBITaxonomy database identifier.
Special cases of adjectives being used to indicate a taxon, misspellings, typographic or other errors and enumerations were indicated as such.
Taxonomic mentions that did not correspond to an existing NCBI Taxonomy database entry were also indicated.

Additional guidelines for the annotation of the S1000 corpus

The first resource that is trusted to resolve issues is NCBI Taxonomy. If there is still not enough information there we have resolved inconsistencies using the Catalogue of Life, ICTV, ITIS, Avibase and WoRMs.
The NCBI Taxonomy Ranking has been adopted from Schoch, et. al, 2020

General annotation guidelines

Taxonomic mentions that correspond to Species, Genus and Strain will receive annotations and normalization to taxonomy reference databases (priority will be the normalizations to NCBI taxonomy, and when that’s not possible the resources mentioned above will be used)
Adjectival forms like murine (taxid:10090), bovine (taxid:9913), pneumococcal (taxid:1313) that map to a specific species should be annotated as such
The role in which common species names are mentioned should not be taken into account and all species names mentions should be annotated (e.g. rice mentioned as food or tobacco as cigarettes should still be annotated).
Genus or higher level mentions (e.g. Arabidopsis, yeast) should only be annotated as the real taxinomic level (or not annotated at all), and not as synonyms of species names. (e.g. Arabidopsis should be annotated as Genus and assigned the genus taxid:3701)
```
The second face of a known player: Arabidopsis silencing suppressor AtXRN4 acts organ-specifically
T1 Genus 35 46	Arabidopsis
N1	Reference T1 Taxonomy:3701	Arabidopsis
```
Former Species annotations in the original S800 coprpus that belong to the Genus taxinomic rank have been annotated as the latter in the corpus. Ranks higher than Genus (e.g. Phylum, Kingdom, Class, Order, Family) should receive an OOS annotation or not be annotated at all
For annotations above Species only the “coarse” ranks should be considered, thus mapping mentions at fine-grained levels to their coarse equivalents, e.g. Subgenus should be mapped back to Genus.
For Subspecies mentions: when a subspecies name immediately follows a species name the entire mention is simply annotated as one slightly longer Species mention, e.g. Phocoenoides dalli dalli annotated as Species + taxid: 9745 (Rank: Subspecies).
Biotypes should be treated the same way as Subspecies, i.e. they are annotated as Species

common name (scientific name)” mentions should be annotated as two mentions e.g from PMID: 21054435:

We studied seasonal dynamics in delta^1^3C of CO2 efflux (delta^1^3C(E)) from non-leafy branches, upper and lower trunks and coarse roots of adult trees, comparing deciduous Fagus sylvatica (European beech) with evergreen Picea abies (Norway spruce).
T1 Species 174 189 Fagus sylvatica
T2 Species 191 205 European beech
T3 Species 222 233 Picea abies
T4 Species 235 248 Norway spruce

Species names in noun phrase premodifier positions (e.g. Arabidopsis EDR1, Aspergillus nidulans cells) also in cases where they appear as part of the name of an entity of a non-organism type (e.g. human epidermal growth factor receptor 2 (HER2)) are annotated.
Species names are annotated when they are part of hyphenated compound words (e.g. human-infecting)
Clade mentions will receive Clade normalizations and will be assigned type according to nearest non-Clade ancestor (if that falls within the scope of the current annotation effort)
Similarly, no rank mentions will receive no rank normalizations and will be assigned type according to nearest ranked ancestor (if that falls within the scope of the current annotation effort)

Rules for common names

In general, when a Species and a higher-level entry in the taxonomy (e.g. Genus) share a common name or synonym, the Species interpretation should be preferred when it is not clear from context which is intended.
Common names like human, goat, horse, and rats should be always annotated.
Common names that should be annotated in the Genus level:
- fire ant: Genus and taxid:13685 (Solenopsis); Note: red fire ant, little fire ant, black fire ant etc should be tagged as the corresponding species)
- sunflower: Genus+taxid:4231 (Helianthus)
- galaxias : Genus+taxid:51242 (Galaxias)
Common names that should be annotated in the Species level (but could be annotated in a higher taxonomic level):
- rat: synonym for Rattus norvegicus and Rattus. Should be annotated as Rattus norvegicus (taxid:10116), unless explicitly referring to a different taxonomic unit (e.g. cotton rat: Genus + taxid:42414 (Sigmodon))
- fruit fly: synonym for Drosophila melanogaster and Drosophila genus and Tephritidae family. Should be annotated as Drosophila melanogaster (taxid:7227), unless explicitly referring to a different taxonomic unit
- bee: synonym for Apis mellifera, and Apoidea superfamily. Should be annotated as Apis mellifera (taxid:7460), unless explicitly referring to a different taxonomic unit (e.g. bumble bee)
- duck: synonym for Anas platyrhynchos, but can be a synonym for other Anatidae. Should be annotated as Anas platyrhynchos (taxid:8839), unless explicitly referring to a different taxonomic unit
- midge: synonym for Chironomus thummi, but can refer to several species of flies. Should be annotated as Chironomus thummi (taxid:7154), unless explicitly referring to a different taxonomic unit

Mentions that should NOT receive annotations

Adjectival forms of Phyla (e.g. cyanobacterial: taxid:1117) can only be annotated as OOS or not be annotated at all
Adjectival forms of Kingdoms (e.g. viral, bacterial) can only be annotated as OOS or not be annotated at all
Non-name mentions (e.g. woman) and species clues (e.g. patients, children, men, women) should not be annotated. This includes the non-name mention man which should not be annotated as a synonym for Homo sapiens (taxid: 9606)
Mentions that are not monophyletic (e.g. fish) should be annotated as Out-of-scope (OOS) with Note: not monophyletic or not be annotated at all

Forms identified by place names, like ecotype, are not annotated.

For investigating cadmium uptake, we incubated protoplasts obtained from leaves of Thlaspi caerulescens (Ganges ecotype) with a Cd-specific fluorescent dye.
T1 Species 83 103 Thlaspi caerulescens

Species names are NOT annotated when they appear as a substring in a word not separated by a boundary such as a hyphen (e.g. nonhuman)
Abbreviations are marked if the abbreviation stands for an organism mention in scope of the annotation, but not if the full form merely includes an organism mention e.g. in modifier position. For example, the H in HER2 is not annotated despite it standing for human.

Cultivars should be annotated as OOS or not be annotated at all.

The physiological traits underlying the apparent drought resistance of 'Tomatiga de Ramellet' (TR) cultivars.
T1 Out-of-scope 72 92 Tomatiga de Ramellet

Rootstocks should be annotated as OOS e.g. in PMID: 20837155

Non-taxonomic groupings such as Gram-positive/negative bacteria, marine bacteria or enteric bacteria should not be annotated. e.g.

The redox-sensitive transcription factor SoxR in enteric bacteria senses and regulates the cellular response to superoxide and nitric oxide.

Oscillochloris trichoides is a mesophilic, filamentous, photoautotrophic, nonsulfur, diazotrophic bacterium which is capable of carbon dioxide fixation via the reductive pentose phosphate cycle and possesses no assimilative sulfate reduction.
T1 Species 0 25 Oscillochloris trichoides

tree and bush are non-taxonomic mentions and thus not annotated or annotated as OOS + Note: non-taxonomic
Standalone alga (algae, microalgae, macroalgae): can only be annotated as OOS + Note: non-taxonomic or not be annotated at all e.g. Algae is an informal term for a large and diverse group of photosynthetic eukaryotic organisms.
protist (any eukaryotic organism that is not an animal, plant, or fungus) is a non-taxonomical expression and can be annotated as OOS + Note: non-taxonomic or not be annotated at all e.g.
protozoa can also be annotated as OOS + Note: non-taxonomic or can not be annotated at all
methanotroph is a non-taxonomical expression and can be annotated as OOS + no taxid or not be annotated at all e.g.
methanogen(s) over 50 Archaea species can be annotated as OOS with Note: not monophyletic or not be annotated at all
prokaryotes includes Bacteria and Archaea in the current three-domain system, so this can be annotated as OOS + no taxid or not be annotated at all e.g.
heterokonts and alveolates are clades of microorganisms and can be annotated as OOS + taxid:33634 and taxid:33630 respectively or not be annotated at all e.g. and e.g.
cyanobacteria, eubacteria and the like can be annotated as OOS or not be annotated at all unless it’s clear from context that the reference is definitely to the genus Cyanobacterium or Eubacterium respectively.
Non-taxonomic groupings of organisms by their behaviour (e.g. herbivores, predators, parasites) should not receive an annotation or should receive an OOS annotation
actinorhiza(l), mycorrhiza(l), ectomycorrhiza can be OOS + Note: non-taxonomic or not be annotated at all
species complex and clonal complex rank can be OOS or not be annotated at all

Rules for common names

Common names that should not be annotated in the Species level:
- ant(s): OOS+taxid:36668 (Formicidae) or no annotation
- insect(s): when standalone assign OOS+taxid:50557 (Insecta) or no annotation
- mite: OOS+taxid:6933 (Acari subclass) or no annotation
- trout: several species of fish, annotate as OOS + no taxid or no annotation
- leafminer and leaf miner: insects that eat the tissue of plants, annotate as OOS + Note: non-taxonomic or no annotation
- fishes: OOS (Clade-like concept, non-tetrapoda vertebrata) or no annotation
- bug: OOS + Note: non-taxonomic or no annotation
- field cricket: OOS + Note: non-taxonomic or no annotation
- mirid bug: OOS+taxid:30084 (Miridae) or no annotation
- clownfish: OOS+taxid:30863 (Pomacentridae) or no annotation
- elephant: 3 species, not monophyletic (both Elephas and Loxodonta genera), annotate as OOS + no taxid or no annotation
- crab: infraorder containing 850 species, so it should be annotated as OOS + taxid:6752 (Brachyura) or no annotation
- grass: OOS+taxid:4479 (Poaceae) or no annotation
- seabird(s): OOS with Note: non-taxonomic or no annotation
- marsupial (animals carry the young in a pouch) is a mammalian clade, e.g. and will be annotated as OOS + taxid:9263 or not annotated at all
- coral(s): Hexacorallia + Octocorallia, but paraphyletic because sea anemones are also part of Hexacorallia: annotated as OOS with Note: not monophyletic or not annotated
- DNA viruses, RNA viruses map to no rank entries: annotated as OOS or not annotated at all
- dsRNA mycoviruses: OOS with Note: non-taxonomic
- cereal: OOS with Note: non-taxonomic
- kittiwake: OOS and Note: non-taxonomic
Young animals (e.g. chicks, calfs etc) should not receive an annotation or should receive an OOS annotation

Special rules for Strains

Strain aliases such as CC-12301(T) (=DSM 45298(T) =CCM 7727(T)) should be annotated in all instances as type Strain.

name strain mentions should be annotated as two mentions of Species+Strain, e.g. from PMID: 20154326

Strain GSW-R14(T) exhibited 97.6 % 16S rRNA gene sequence similarity to F. gelidilacus LMG 21477(T) and similarities of 91.2-95.2 % to other members of the genus Flavobacterium
T1 Species 7 14 GSW-R14
T2 Species 72 86 F. gelidilacus
T3 Strain 87 96 LMG 21477

mentions of the form [Genus] sp. [Strain], should have a separate Genus and Strain annotation e.g.
descriptive references to Strains using gene names are not annotated as organisms e.g.

Special rules for Viruses

Viruses (or other taxonomic units) that have species level of entry as “unidentified” (e.g. “retrovirus” taxid:31931 (“unidentified retrovirus” equivalent: “retrovirus”) or “adenovirus” taxid:10535 (“unidentified adenovirus” equivalent: “adenovirus”)) should NOT be annotated in the Species level.
The following mentions should be annotated as OOS or not be annotated at all:
- “virus”/”viral” OOS+taxid:10239 “Viruses” superkingdom
- “retrovirus” OOS+taxid:11632 “Retroviridae” family
- “influenza virus” OOS+taxid:11308 “Orthomyxoviridae” family
- “herpesvirus” OOS+taxid:10292 “Herpesviridae” family
- “adenovirus” OOS+taxid:10508 “Adenoviridae” family
- “baculovirus” OOS+taxid:10442 “Baculoviridae” family
- “reovirus” OOS+taxid:10880 “Reoviridae” family
The following mentions should be annotated as Genus:
- “norovirus” Genus+taxid:142786 “Norovirus” genus
- “ebola virus” Genus+taxid:186536 “Ebolavirus” genus
- “cytomegalovirus” Genus+taxid:10358 “Cytomegalovirus” genus
dengue: dengue is synonym for dengue fever (disease), annotate as OOS + no taxid unless dengue virus is mentioned when it should be annotated as taxid:12637 (Species)
smallpox: smallpox is synonym for smallpox disease, annotate as OOS + no taxid unless smallpox virus is mentioned when it should be annotated as taxid:10255 (Species)
influenza: influenza is synonym for the flu (disease), annotate as OOS + no taxid unless influenza X virus is mentioned when it should be annotated as Species. EXCEPTION: standalone influenza may be marked when organism sense is clear from context (e.g. influenza strains)
human adenovirus (or similar cases): when a mention cannot be normalized in an “identified” virus species it should be annotated e.g. as Species+taxid:9606 (Homo sapiens) for human and OOS+taxid:10508 (Adenoviridae) for adenovirus (or no annotation for the latter)

Special rules for Yeasts

All text spans including “yeast” should have an OOS annotation if the taxonomy level is higher than Genus or should not be annotated at all:
- standalone yeast: OOS+taxid:147537 (“true yeast” subphylum) (Note: an even higher level may be included)
- black yeast: OOS+taxid:34395 (“black yeast” order)
- budding yeast: OOS+taxid:4892 (“budding yeasts” order)
- fission yeast: OOS+taxid:4894 (“fission yeasts” family)
- truffle: Genus + taxid:36048 (Tuber genus)

Special rules for Amoebae

All amoebae instances have been revised to resolve confusion of non-taxonomical expression amoebae (type of cell or unicellular organism which has the ability to alter its shape), of taxid:554915 (OOS: Clade: Amoebozoa), and taxid:55774 (Genus: Amoebae). Most of the cases were non-taxonomical expressions (OOS + no taxid)
- testate amoebae: very common combination of mentions, which means shelled amoebae, which explains the form of microorganism(s): OOS + no taxid or no annotation
- Interesting article PMID: 21112814, where both non-taxonomical and Genus amoebae are mentioned (only one real “amoebae” Genus in the corpus)

Special cases

Four mentions of “astomes” in this document PMID: 21398102 are OOS
Astome ciliates in this document PMID: 21398102 are also OOS
FGSC should not be annotated as it refers to a complex which is OOS, namely Fusarium graminearum complex PMID: 22004876
Mentions of carnivores in PMID: 21323921 are OOS (interpreting these to refer generally to meat-eating animals)
human and primates in a context of non-human primates are considered two mentions 21295520
PMID: 2435057 is discussing retroviruses, but terminology there is quite old (published in 1987). ICTV (International Committee on Taxonomy of Viruses) was used to figure out how those viruses are called/classified in that period tracing its history.
GII.4 in PMID: 20980508 has been annotated as Species, following the general rule about Clade mentions
arbuscular mycorrhizal fungi (AMF) e.g. in PMID: 20880038 is OOS
tropical japonica rice (e.g. PMID: 20946420): following rule about no rank entries: normalization to NCBI txid: 1736656 and type Species

Span consistency guidelines

The expressions sp. nov. and gen. nov., sp. nov. are not included in the Species name, since these are supposedly used only the first time a genus and/or a species/subspecies is described to denote that it’s new, so they are not part of the scientific name and shouldn’t be found anywhere else other than the first paper describing them.
An annotated span should not end with sp. or spp.
Superscript T - to denote type strain - should not be included in species’ names
The person’s name should not be included in the species name, especially when it is in parentheses. The non-parenthesized form is a bit more complex (at least in the example above Pseudacteon tricuspis Borgmeier is a valid name shown as a synonym for Pseudacteon tricuspis in NCBI taxonomy). For annotation consistency the suggestion is to drop these names in all appearances. (The confusion with subspecies can be avoided because of the capital letter at the start of the second word, e.g. Ursus arctos arctos would be easy to distinguish from Ursus arctos Linneaus and then drop the name for the latter.)
Do not include common head nouns such as “plants” in annotation spans
Do not include adjectival premodifiers such as “native” in annotation spans
Model words like SCID mouse should be excluded from annotations

“species complex” should not be part of a species name, e.g. from PMID: 20682355

The splicing activity of the PRP8 intein from the B. dermatitidis, E. parva and P. brasiliensis species complex was demonstrated in a non-native protein context in Escherichia coli.
T5	Species 50 65	B. dermatitidis
T6	Species 67 75	E. parva
T7	Species 80 95	P. brasiliensis
T8	Species 164 180	Escherichia coli

f. sp. (forma specialis) should be included in the annotated mention (e.g. Blumeria graminis f. sp. tritici)
Do not include nouns identifying levels of taxonomy in annotation spans. For example, the words strain, serotype, serovar, and serogroup should be excluded from the spans of annotated Strain mentions. e.g from 20154326
```
Strain GSW-R14(T) exhibited 97.6 % 16S rRNA gene sequence similarity ...
T1 Strain 7 14 GSW-R14
```
Annotate antibodies e.g anti-HCV with species annotation for the organism (HCV) and Note: “anti-“ prefix

For information on Annodoc, see http://spyysalo.github.io/annodoc/.