dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements. We thank the anonymous referee for very helpful comments and suggestions. C. Y. was supported by an  ESO  Fellowship. C. Y. thanks  Johan Richard  and  Martin Bureau  for insightful discussions, and also thanks  John Carpenter  and  Edward Fomalont  for discussion on ALMA data reduction. This paper makes use of the following ALMA data: ADS/JAO. ALMA# 2015. 1. 01320. S and # 2013. 1. 00358. S. ALMA is a partnership of  ESO  (representing its member states),  NSF (USA)  and  NINS (Japan) , together with  NRC (Canada) ,  MOST  and  ASIAA (Taiwan) , and  KASI (Republic of Korea) , in cooperation with the  Republic of Chile. The Joint ALMA Observatory is operated by  ESO ,  AUI/NRAO , and  NAOJ. C. Y. and Y. G. acknowledge support by  National Key R&D Program of China  ( 2017YFA0402700 ) and the  CAS Key Research Program of Frontier Sciences.
R. G. , C. Y. , and A. O. acknowledge the  Programme National Cosmology and Galaxies  for financial support in the early stages of this project. C. Y. , A. O. , and Y. G. acknowledge support from the  NSFC  grants  11311130491  and  11420101002. C. Y. , A. O. , A. B. , and Y. G. acknowledge support from the  Sino-French LIA-Origins joint exchange program. I. R. S. and A. M. S. acknowledge support from  STFC  ( ST/P000541/1 ). S. D. is supported by the  UK STFC  Rutherford Fellowship scheme. E. I. acknowledges partial support from  FONDECYT  through grant N • 1171710. E. G. -A. is a Research Associate at the  Harvard-Smithsonian Center for Astrophysics , and thanks the  Spanish Ministerio de Economía y Competitividad  for support under projects  FIS2012-39162-C06-01  and  ESP2015-65597-C4-1-R , and  NASA  grant  ADAP NNX15AE56G.
RJI acknowledges support from  ERC  in the form of the Advanced Investigator Programme, 321302, COSMICISM. H. F. acknowledges support from  NSF  grant  AST-1614326. D. R. acknowledges support from the  National Science Foundation  under grant number  AST-1614213. M. N. acknowledges financial support from the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No  707601. M. J. M. acknowledges the support of the  National Science Centre, Poland , through the  POLONEZ grant   2015/19/P/ST9/04010 ; this project has received funding from the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No. 665778. I. P. -F. acknowledges support from the  Spanish  grants  ESP2015-65597-C4-4-R  and  ESP2017-86852-C4-2-R.
Complex carbohydrates-oligosaccharides and polysaccharides of diverse residue and linkage composition-are central to a wide range of biological processes, such as energy storage, inflammation, host-pathogen interactions, diseases, and differentiation/development  (1). Not least, manifold complex carbohydrates play essential structural roles in the cell walls in terrestrial and marine biomass  (2, 3). These biomass sources represent major sinks in the global carbon cycle (4, 5) and a vast renewable resource for the production of energy, chemicals, and materials  (6). The synthesis, rearrangement, and ultimate saccharification of the vast diversity of glycosidic linkages in natural carbohydrates require a correspondingly broad range of specific carbohydrate-active enzymes (CAZymes). 4 In light of the continually accelerating rate of sequence data deposition, the CAZy database has emerged as a central resource uniting specificity, mechanistic, and structural information within actively curated, sequence-based families of glycosyltransferases, glycoside hydrolases (GHs), polysaccharide lyases, carbohydrate esterases, auxiliary activity enzymes, and associated noncatalytic carbohydrate-binding modules (CBMs)  (7, 8).
In such cases, division into subfamilies based on molecular phylogeny has been shown to significantly increase predictive power in a handful of GH and polysaccharide lyase families previously  (9 -13). However, a major limitation of large-scale phylogenetic analyses is the dependence on a highly accurate multiple sequence alignment (MSA)  (14)  and subsequent phylogenetic tree estimation, in which the computational complexity increases exponentially with the number of sequences  (15). As the number of nonredundant sequences in the CAZy database increases  (7) , highly accurate subfamily phylogenies will be infeasible for most families in the foreseeable future. Sequence similarity networks (SSNs), which are conceptually illustrated in Fig. 1 , offer a potential solution to this conundrum. In contrast to MSA-based phylogenies, SSNs are based on all-versus-all pairwise local sequence alignments, the computational requirements of which scales linearly with the number of sequences and are easily amenable to parallelization.
GH16 members are united by a compact (ϳ30 kDa) ␤-jelly roll structural fold  (26) , which nonetheless has a remarkable evolutionary plasticity that gives rise to specificities for a plethora of complex terrestrial and marine cell-wall carbohydrates, hydrolase and transglycosylase activities, and noncatalytic substrate-binding functions  (21, (27) (28) (29). Presently, GH16 comprises ϳ8,000 sequences in the public CAZy database representing 15 known activities  (7) , which is comparable with other large families (GH5 and GH43) for which subfamily classifications have been established (GH13 is an exception, with nearly 10-fold more members, whereas GH30 is 4-fold smaller than GH16) (9 -13). Only 2. 5% of GH16 sequences have been enzymatically characterized  (7) , which challenges functional prediction.
Here we present a comprehensive subfamily classification of GH16 based on large-scale SSN analysis of the entire GH16 sequence space as a roadmap for future functional glycogenomics. The subfamily topology was equal to that obtained by classical phylogenetic analysis of a reduced sequence data set. The resulting robust subfamilies were used in turn to generate hidden Markov models (HMMs), which will form the basis for the automated incorporation of new sequences into the continually expanding CAZy database.
Subfamily delineation All-versus-all pairwise local sequence alignments were calculated for 22,946 GH16 domain sequences from the CAZy database in 210 min on a desktop computer (Intel Xeon Processor E5-1620 v4, 8 cores, 3. 5 GHz, 16 GB RAM). For comparison, the computational time was reduced to 13 min using 128 cores on Compute Canada's WestGrid high-performance infrastructure. Subsequently, the BLAST result file was indexed over thresholds in intervals of 5 log units for E values between 10 Ϫ5 and 10 Ϫ120. Our preliminary SSN and HMM analyses indicated that the 10 SSNs for E-value thresholds between 10 Ϫ20 and 10 Ϫ65 were of most interest with the number of subfamilies ranging from 3 at E ϭ 10 Ϫ20 to 27 at E ϭ 10 Ϫ65 (Fig. 2 ). Mapping.
GH16 subfamilies from the phylogenetic tree (Fig. 5A ). Importantly, all clades comprising individual subfamilies are supported by high bootstrap values. The SSN analysis delineated GH16 sequences into "characterized" subfamilies with one or more biochemically or structurally characterized members (denoted in the CAZy database  (7) ) and "uncharacterized" subfamilies for which structuralfunctional data are currently lacking. Table  1  summarizes the taxonomic range of source organisms, experimentally determined enzyme activities, and available tertiary structures for each subfamily shown in Fig. 4A. Specific sequence accessions, including subfamily membership and characterization details, may be accessed directly in the CAZy database (http://www. cazy. org/GH16. html) (7). 5  In total, 16 of 23 subfamilies contained at least one biochemically characterized member, and 11 had a three-dimensional structure representative.
4. 1. -) (32). Structurally, GH16_1 is defined by the presence of numerous helical elements on the core ␤-jelly-roll fold: two in the N-terminal region and four in the C-terminal region, most of which are located on the opposite side of the structure from the active site cleft (Fig. 5B ). The ␣5 helix carries a conserved tryptophan, Trp-257 (PDB code 2CL2 (33)), that points into the active site and faces a loop, which is consolidated by a disulfide bridge. Together, these elements define the positive enzyme subsites  (34)  in this subfamily. A notable sequence pattern "WPA. WPX" (X is often Y or N, but also A, T, or I) is shared with GH16_3 and GH16_9 members. The WPX motif is located in a loop bordering the active-site cleft at the negative subsites and therefore likely contributes to substrate specificity.
The broad taxonomical diversity of GH16_3 members makes this subfamily particularly sensitive to the threshold E-value cutoff, such that increasingly strict cutoff values result in fragmentation along taxonomic lines. The large sequence and taxonomic diversity is reflected by low structural homology in this subfamily, where only very few stretches and features are strictly conserved among the subfamily members. However, the sequence pattern "WPA. WXX. WPX" (X being M or L for the second motif and A, K, R, M, or L for the third motif), similar to that found in GH16_1, is largely conserved throughout members of this subfamily. In GH16_3, this loop faces a short, subfamily-specific -helical element that is located in the N-terminal region (residues 25 to 34 in PDB code 4CTE  (37) ). Furthermore, a tryptophan or phenylalanine that lines the active site in the positive subsites is part of a partially conserved motif present in many subfamily members, as is a loop (His-155 to His-163) that contains a strongly con-Figure  5.
Phylogenetic tree and structure-function relationships of GH16. A, maximum-likelihood phylogenetic tree was generated using up to 30 representative sequences for each GH16 subfamily defined by the sequence similarity network shown in Fig. 4. Three GH7 cellulases (GH7 and GH16 constitute clan GH-B)  (7)  were used to root the tree. Bootstrap values based on 100 replicates are shown. The tree separates (indicated by a line) GH16 enzymes with the ␤-bulge active-site motif EXDXXE from those with the ␤-strand active-site motif EXDXE, concordant with previous analyses  (30, 51). Branch coloring is identical to that used in Figs. 2  and 4 ; subfamily numbering and mnemonics are given in Fig. 2. Subfamily membership of all GH16 members is available on the actively curated CAZy database (http://www.
Although this observation contravenes our usual strict requirement for taxonomic diversity to establish a subfamily, the early segregation of this group at comparatively high E values (Fig. 2 ) supports the creation of a robust subfamily. Presently, biochemical function has not been defined for any GH16_9 member, but five members have been structurally characterized. A structural characteristic of this subfamily is the low content of helical elements (Fig. 5B ), in which only a short helix is present in the N-terminal region adjacent to the first loop near the negative subsites. Remarkably, GH16_9 members generally lack aromatic residues in the negative subsites as compared with other subfamilies. A tryptophan (Trp-154 in PDB code 4PQ9 (unpublished)) present in a conserved loop is positioned to accommodate a substrate in the positive subsites.
This loop contains a characteristic arginine residue (Arg-70 in PDB code 3JUU  (39) ) in addition to a conserved tryptophan, Trp-67, that is also present in GH16_16, both of which are involved in substrate binding. The loop formed by a conserved sequence motif close to the C terminus (residues 256 -265 in PDB code 3JUU) is also structurally distinct from those in other subfamilies. GH16_12-Like GH16_11, GH16_12 is composed exclusively of bacterial members from the Bacteroidetes phylum, except for one member from Coraliomargarita (Verrucomicrobia). GH16_12 contains three biochemically characterized ␤-porphyranases (EC 3. 2. 1. 178). GH16_11 and GH16_12 are highly related and form a uniform subfamily at lower thresholds, precisely resolving into two subfamilies at the SSN threshold of E ϭ 10 Ϫ55 (Figs.
2  and 4 ). Consistent with the high relatedness of the two subfamilies, the major characteristic structural features are shared between the two subfamilies, including the N terminus and the first loop bordering the negative subsites. GH16_12 is distinguished by specific amino acid substitutions in the aromatic platform of the Ϫ1 subsite, as well as various loops throughout the tertiary structure. Specifically, a loop between the C-terminal two ␤-strands shared with GH16_11 is distinguished by sequence motives that are not identical between the two subfamilies, namely the stretch from residues 221 to 230 is WNPVPK-DGGM in PDB code 3JUU, whereas the structurally identical stretch from residues 288 to 297 is WEKQVPTAED in PDB code 4AWD  (40). Additionally, the motif comprising residues 210 to 228 in 4AWD, which in many other subfamilies forms a ␤-strand that terminates the ␤-sheet at the positive subsites, has a characteristic structure in GH16_12 members.
GH16 subfamilies the bacterial kingdom. No tertiary structural representatives currently exist in GH16_13. GH16_15-Two ␤-agarases (EC 3. 2. 1. 81) have been reported in the small GH16_15 (currently 24 members). This subfamily is very distinct from the other ␤-agarase-containing subfamily, GH16_16 (Fig. 2 ), to which it forms a sister clade with high bootstrap support (Fig. 5A ). A member of GH16_15 has recently been shown to hydrolyze specifically complex agars from Ceramiales species, functionally distinguishing this subfamily from GH16_16  (42). Notably, unlike GH16_16, no CBMs are associated with GH16_15. Together with functional characterization, the first structural representative of GH16_15 has recently been solved (PDB code 6HY3)  (42). This structure reveals high structural similarity with GH16_16, with differences mainly observed in specific amino acid substitutions.
Particularly notable are two aromatic residues (Trp-110 and Tyr-112 in PDB code 6HY3) that are located in the negative binding subsites and a characteristic loop (residues 291-300) located near the positive binding subsites, which presents two tryptophan residues (Trp-291 and Trp-297) that point into the active-site cleft. Another unique feature of GH16_15 is the presence of a conserved arginine (Arg-186) near the active site EXDXXE motif, as well as a second strictly conserved arginine (Arg-224) located in the positive subsites. GH16_16 -Considering the size of GH16_16 (153 sequences), it is the most densely studied subfamily in GH16 with 32 biochemically characterized ␤-agarases (EC 3. 2. 1. 81) from Bacteroidetes, Proteobacteria, and Actinobacteria. A CBM13 or CBM6 is found associated with approximately half of the GH16_16 members.
In GH16_16 a characteristic N terminus is followed by an ␣-helix (Gly-94 -Glu-99 in PDB code 4ATF  (43) ). This helix is not directly bordering the active site groove; however, it is immediately followed by a GH16_16-specific loop that contains a well-conserved tryptophan residue (Trp-109) constituting subsite Ϫ3. Another characteristic feature of GH16_16 is the C-terminal motif from residues 308 to 315 that also presents an ␣-helix providing a tryptophan that forms the ϩ3 subsite. Opposite of this feature is a loop including residues His-215-Phe-222, which contains a strictly conserved arginine residue (Arg-219) that is involved in binding the 3,6-anhydro bridge of agarose in subsite Ϫ2. GH16_17-GH16_17 contains -carrageenases (EC 3. 2. 1. 83) from both Proteobacteria and Bacteroidetes. GH16_17 is the most distinct subfamily among those that hydrolyze marine carbohydrates, because it segregates at comparatively high E-value thresholds (Figs.
5B ). Otherwise, a key feature of this subfamily is vast diversity in which only few elements are strictly conserved. A notable differentiator is found in the loop that follows the conserved tryptophan comprising the Ϫ1 subsite, which contains a well-conserved tyrosine or phenylalanine (Tyr-143 in PDB code 5OCR) (  44 ) that provides a hydrophobic environment to accommodate the 3,6-anhydro bridge in the Ϫ2 subsite. Importantly, a loop that is stabilized through two anti-parallel ␤-strands is positioned directly above the Ϫ1 subsite, thereby providing a strictly conserved arginine (Arg-263) to bind the -carrageenan-specific sulfate group on O4 of galactose residues. GH16_17 members have sequence variation around the positive subsites, indicating that subtle differences in substrate specificity might be found among this divergent subfamily.
GH16_18 -GH16_18 is a large subfamily with 2,576 members. The subfamily is entirely composed of fungal enzymes including biochemically characterized chitin ␤(1,3)/␤(1,6)-glucosyltransferases (EC 2. 4. 1. -) and cell-wall modifying enzymes (EC 3. 2. 1. -/2. 4. 1. -). GH16_18 have a characteristic N terminus, starting with a disulfide bridge (residues 25-40 in PDB code 6IBW (unpublished)), which is arranged into a triple-stranded ␤-sheet with the C terminus. Strikingly, no residues from this loop appear to participate to substrate binding in the negative subsites. On the other hand, one strictly conserved tryptophan, Trp-207, forms a platform at the Ϫ2 subsite and the positive subsites also contain one strictly conserved tryptophan residue (Trp-221) and two largely conserved aromatic residues (Phe-137 and Tyr-145) that form large hydrophobic platforms to accommodate the substrate.
No tertiary structural representatives currently exist in GH16_19. GH16_20 -GH16_20 is a well-characterized subfamily composed of plant enzymes specific for xyloglucan  (46). Members of this subfamily are either xyloglucan endo-transglycosylases (XETs, EC 2. 4. 1. 207) or xyloglucan endo-hydrolases (EC 3. 2. 1. 151) (28, 47). A significant key feature of GH16_20 is the addition of a large C-terminal domain (residues 232-264 in PDB code 2VH9  (48) ; InterPro and PFAM "XET_C") that extends the active-site cleft at the positive subsites. In addition, a well-conserved loop region (residues 181-190) is located immediately adjacent to.
Consequently, characteristic features of this subfamily are short loops surrounding the substrate-binding groove. The conserved stretches are concentrated in four regions that border the central cleft, two on each side, which contain aromatic residues important for substrate binding (Tyr-24, Tyr-94, Trp-103, and Trp-192 in PDB code 1GBG)  (54). Two of the characteristic loops contain short helical segments; the first (residues 91-100) is located at the Ϫ1 subsite, directly preceding the active site EXDXE motif, whereas the second borders the active site on the opposite side (residues 189 -193), thereby providing a strictly conserved tryptophan at the ϩ1 subsite. In addition, and similar to the GH16_20 subfamily, the aromatic platform at the Ϫ1 subsite in GH16_21 members is a phenylalanine (Phe-92), not a tryptophan.
Nonclassified sequences Roughly 3% of the analyzed GH16 sequences were not assigned to subfamilies (Fig. 2 ), primarily because of a lack of a sufficient number of orthologs in the CAZy database to define a subfamily with at least 20 members and sufficient taxonomical diversity. Among these is the only characterized GH16 member from a virus (Paramecium bursaria Chlorella virus 1, Gen-Bank TM accession no. AAC96462. 1), which is an endo-␤(1,3)/ ␤(1,4)-glucanase that is distant from, but most closely related to, members of subfamily GH16_3. Other examples include two small groups related to the GH16_11 and GH16_12 ␤porphyranase subfamilies, containing eight members and one biochemically characterized ␤-porphyranase each: ␤-porphyranase A (PDB codes 3ILF and 4ATE)  (39, 43)  and ␤porphyranase C, respectively, from Zobellia galactanivorans DsijT.
Advantages and limitations of SSN-based subfamily classification The utilization of a sequence similarity network-based approach allowed the division of 22,946 GH16 catalytic modules into subfamilies in a scalable, computationally efficient manner. Comparatively rapid generation of an all-versus-all pairwise scoring matrix, facile generation of SSNs at increasing BLAST E-value thresholds, and analysis of precision and recall rates guided the selection of an SSN cutoff value producing 23 robust subfamilies (Figs. 2  and 4A ). A particular advantage of the SSN-based approach versus classical phylogenetic methods based on MSAs is the ability to utilize the full sequence data set without the need for down-sampling to reduce computation time. For example, the previous division of GH5  (9)  and GH43 (12) into subfamilies based on molecular phylogeny coped with the large amount of sequences (2,333 and 4,455, respectively) by employing the common practice of initial clustering of similar sequences, using algorithms such as UCLUST and CD-Hit  (55, 56)  to reduce the data sets.
Looking to the future: emerging subfamilies The CAZy database is derived exclusively from the NCBI GenBank TM daily releases for practical reasons  (7). Consequently, CAZy database, and thus the entire GH16 sequence set used here, does not capture sequences from nascent (meta)genomic efforts, especially unfinished genomes from sequencing center databases (e. g. Joint Genome Institute, Broad Institute, Beijing Genomics Institute, etc. ). Thus, it can be reasonably anticipated that the number of GH16 subfamilies will increase beyond the 23 presented here as the number of sequences in GenBank TM continues to increase. This.
GH16 subfamilies includes subfamilies from currently identified groups with fewer than 20 sequences or currently low taxonomic diversity, as well as newly emergent subfamilies from currently unexplored sequence space. An example of an emerging GH16 subfamily is comprised of recently identified mixed-function endo-␤(1,3)/␤(1,4)-glucanases/endo-xyloglucanases from plants, for which biochemical and structural information exists (e. g. PDB code 5DZF and 5DZG)  (51). These EG16 (endo-glucanase, GH16) members represent functional intermediates and an evolutionary link between the classic bacterial endo-␤(1,3)/␤(1,4)-glucanases in GH16_21 and the plant xyloglucan endo-transglycosylases and endo-hydrolases in GH16_20  (50, 51). A comprehensive census using genomes and transcriptomes of over 1,200 plant species has revealed a large collection of EG16 sequences in plant sequence databases, which are currently not deposited in Gen-Bank TM  (23).
CODA Since the introduction of protein SSN analysis in its present form a decade ago  (16) , the use of SSNs has been growing in popularity for the analysis of large data sets  (17, (66) (67) (68) (69) (70) (71) (72) (73) (74) , in part because of a lower computational demand than classical molecular phylogeny. Here, we have utilized the power of SSN analysis to devise a robust subfamily classification of the large and diverse family GH16. This framework, which collates biochemical and structural data on characterized members, will enable more refined functional prediction to guide future bioinformatics and experimental studies. Nonetheless, we advocate a conservative approach to protein annotation, in which uncharacterized enzymes are referred to solely by their subfamily membership, to avoid the propagation of misleading functional annotation in public databases.
Data acquisition All GH16 members were extracted from the CAZy database (February 2018)  (7)  and used to retrieve amino acid sequences from GenBank TM. During this step, additional metainformation was gathered, including taxonomic lineage (kingdom, phylum, class, order, family, genus, and species ranks), modularity (presence of CBMs, signal peptides, etc. ) of the full-length sequence (semimanually annotated using in-house CAZy pipelines)  (75) , and both biochemical and structural information from the literature. Sequences with less than 95% coverage to the GH16 family model were considered as fragments (13. 7% in total) and not included in the final data set.