Functional Classification Scheme Research Articles

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

Characterization and Study of Dominated Alluvial Soil Profile of Mirzapur in Indo-Gangetic Plain (IGPs) of India

This provides the basic information necessary to create functional soil classification schemes and assess soil fertility in order to unravel some unique soil problems in an ecosystem. Mirzapur district is situated in the southern part of Uttar Pradesh and is located between 25.8° N to 25.15° N latitude and 82.34° E to 82.58° E longitude covering an area of 4952.5 km2. The soils of the study region comprised of alluvial soil representing Entisol and soils which are formed on granitic parent material representing Alfisols. The coupling of soil characterization, soil classification and soil mapping provides a powerful resource for the benefit of mankind especially in the area of food security and environmental sustainability. Among the cationic micronutrients, Zn content varied between 1-3 ppm in the Mirzapur soil profile. Copper content varied between 1-7 ppm in Jamalpur, 1-4 ppm in Narayanpur. The available Cu content is categorized as sufficient if it is > 0.2 ppm. Available iron content varied between 2-40 ppm in Jamalpur soil profile and 8-63 ppm in the Narayanpur soil profile. Available Mn content varied between 2-40 ppm in Jamalpur, 5-18 ppm in Narayanpur. Soils are generally categorized as having enough manganese in the DTPA extractable Mn content is > 0.2 ppm. Hence all soils of Jamalpur and Narayanpur had sufficient available soil manganese.

Long‐term monitoring shows that drought sensitivity and riparian land use change coincide with freshwater mussel declines

Abstract Freshwater mussels (Bivalvia: Unionoida) are globally imperilled and are the subjects of wide‐ranging conservation initiatives. This study combined traditional species‐monitoring surveys with a novel functional trait classification scheme and publicly available environmental data to assess potential environmental drivers of declining mussel abundance and species richness. Surveys to document mussel abundance and assemblage composition in south‐east Oklahoma, United States were conducted on the Glover, Mountain Fork and upper Little rivers. Present day survey results (2015–2021) were compared with those from previous studies (1993–1999, 2010) to document long‐term changes in the species and functional composition of mussel assemblages and concurrent changes in climate and land use. Mussel catch per unit effort declined by 71.5% between historical and present day surveys. Species richness declined by 44.4% over this same period. Using a novel classification of mussel drought sensitivity, it was found that the declines were associated with a disproportionate loss of drought‐sensitive taxa (67.0% decline) – those classified as drought‐tolerant did not decline in abundance. Mussel declines coincided with the loss of open surface waters (such as streams, ponds and lakes) and riparian wetlands, increased local air temperatures and longer and more intense hydrological drought. These findings indicate that for a complete understanding of the causes and consequences of mussel declines, conservation biologists must not only monitor the species composition and abundance of threatened organisms, but also consider functional traits. The results further underscore the importance of long‐term monitoring for long‐lived organisms owing to the decadal time scales over which climate and land use change occur.

Mapping Drainage Structures Using Airborne Laser Scanning by Incorporating Road Centerline Information

Wide-area drainage structure (DS) mapping is of great concern, as many DSs are reaching the end of their design life and information on their location is usually absent. Recently, airborne laser scanning (ALS) has been proven useful for DS mapping through manual methods using ALS-derived digital elevation models (DEMs) and hillshade images. However, manual methods are slow and labor-intensive. To overcome these limitations, this paper proposes an automated DS mapping algorithm (DSMA) using classified ALS point clouds and road centerline information. The DSMA begins with removing ALS ground points within the buffer of the road centerlines; the size of the buffer varies according to different road classes. An ALS-modified DEM (ALS-mDEM) is then generated from the remaining ground points. A drainage network (DN) is derived from the ALS-mDEM. Candidate DSs are then obtained by intersecting the DN with the road centerlines. Finally, a refinement buffer of 15 m is placed around each candidate DS to prevent duplicate DS from being generated in close proximity. A total area of 50 km2, including an urban site and a rural site, in Vermont, USA, was used to assess the DSMA. Based on the road functional classification scheme of the Federal Highway Administration (FHWA), the centerline information regarding FHWA roads was obtained from a public data portal. The centerline information on non-FHWA roads, i.e., private roads and streets, was derived from the impervious surface data of a land cover dataset. A benchmark DS dataset was gathered from the transport agency of Vermont and was further augmented using Google Earth Street View images by the authors. The one-to-one correspondence between the benchmark DS and mapped DS for these two sites was then established. The positional accuracy was assessed by computing the Euclidian distance between the benchmark DS and mapped DS. The mean positional accuracy for the urban site and rural site were 13.5 m and 15.8 m, respectively. F1-scores were calculated to assess the prediction accuracy. For FHWA roads, the F1-scores were 0.87 and 0.94 for the urban site and rural site, respectively. For non-FHWA roads, the F1-scores were 0.72 and 0.74 for the urban site and rural site, respectively.

Классификация документов архивных фондов городовых магистратов. На примере Курского наместничества второй четверти XVIII века

The article classifies documents of magistrates of the Kursk viceroyalty, which are stored in the State Archive of Kursk Region in the fonds of the Kursk viceroy’s office, Kursk magistrate, and Oboyan magistrate. For studying legal proceedings, demography, and administration in the second quarter of the 18th century, researchers prefer materials of the Kursk Chambers of Civil and Criminal Court, treasury department, and the viceroy’s office. Thus, studying external and internal documentation of magistrates is significant for revealing their role in the cities’ political and economic life. Until the early 1990s, in the Russian historiography there have been no specialized works on composition of documents of magistrates. The use of materials of city courts was thematic. Socio-economic studies put emphasis on a statistical documentation, while legal works focused on established practice in applying the law. Nevertheless, the scholarship of the second half of the 19th century developed two main principles of systematization of magistrate documents: chronologically-nominal and structurally-functional. Historians noted that, despite losing their tax and administrative competencies in the 1780s, magistrates continued to control these issues. The work is to structure documents of city courts of the Kursk viceroyalty. The author has developed her own structural and functional classification scheme, taking into account organizational and competence specifics of these institutions. For this typologization, a contextual analysis of materials has been carried out in order to evaluate the documents’ legal force and to identify which area of relations they regulate. Thus, the documents have been divided in two groups (organizational/administrative and competence-based), each further subdivided in 4 classes. The first block includes materials regulating activities of magistrates (internal and external regulatory legal acts) and those springing from their functioning (accounting, personnel, accounting and registration, reporting documents). The second block includes materials which the magistrates created while executing their direct and indirect powers. The given classification reflects the composition of city courts’ documents and procedures of their clerical work, as well as their place and role in the city development of the Kursk viceroyalty in the second quarter of the 18th century.

Multilevel Feature Fusion-Based CNN for Local Climate Zone Classification From Sentinel-2 Images: Benchmark Results on the So2Sat LCZ42 Dataset

As a unique classification scheme for urban forms and functions, the local climate zone (LCZ) system provides essential general information for any studies related to urban environments, especially on a large scale. Remote sensing data-based classification approaches are the key to large-scale mapping and monitoring of LCZs. The potential of deep learning-based approaches is not yet fully explored, even though advanced convolutional neural networks (CNNs) continue to push the frontiers for various computer vision tasks. One reason is that published studies are based on different datasets, usually at a regional scale, which makes it impossible to fairly and consistently compare the potential of different CNNs for real-world scenarios. This article is based on the big So2Sat LCZ42 benchmark dataset dedicated to LCZ classification. Using this dataset, we studied a range of CNNs of varying sizes. In addition, we proposed a CNN to classify LCZs from Sentinel-2 images, Sen2LCZ-Net. Using this base network, we propose fusing multilevel features using the extended Sen2LCZ-Net-MF. With this proposed simple network architecture, and the highly competitive benchmark dataset, we obtain results that are better than those obtained by the state-of-the-art CNNs, while requiring less computation with fewer layers and parameters. Large-scale LCZ classification examples of completely unseen areas are presented, demonstrating the potential of our proposed Sen2LCZ-Net-MF as well as the So2Sat LCZ42 dataset. We also intensively investigated the influence of network depth and width, and the effectiveness of the design choices made for Sen2LCZ-Net-MF. This article will provide important baselines for future CNN-based algorithm developments for both LCZ classification and other urban land cover land use classification. Code and pretrained models are available at https://github.com/ChunpingQiu/benchmark-on-So2SatLCZ42-dataset-a-simple-tour.

Knee Osteoarthritis Functional Classification Scheme - Validation of Time Dependent Treatment Effect. One Year Follow - Up of 518 Patients

Objective: The purpose of the current study was to validate time dependent changes of a novel functional classification for patients with knee osteoarthritis (KOA), following a home-based biomechanical treatment (HBBT).Methods: A retrospective analysis of 518 patients with KOA was conducted. All patients were classified using a novel knee osteoarthritis functional grade (KOFG) classification for KOA, based on spatio-temporal gait analysis. Patients were re-classified after 3 months and 1 year of HBBT to examine and validate this classification using timedependant changes. The time dependent changes in the classification were compared to gold-standard selfassessment questionnaires, WOMAC and short form 36 (SF-36).Results: The changes in KOFG were demonstrated over time, with most changes occurring after 3 months of treatment with consolidation of the effect at 12 months. For example, of 427 patients that were classified in KOFG 2-4 grade at baseline, 44.9% and 51.5% had lower (better) KOFG grades at 3 and 12 months of treatment, respectively. The changes in KOFG were validated with WOMAC and SF-36 questionnaires showing a significant correlation between KOFG changes and changes in WOMAC and SF-36. SF-36 pain sub-scale showed an improvement of 33.0% and 38.0% following 3 months and 12 months of treatment, respectively (p values <0.0001).Conclusions: The results of the current study validate the knee osteoarthritis functional grade classification scheme as a tool to assess time dependant changes in KOA as well as its sensitivity to assess treatment effect. The KOFG can offer a more robust mode of reporting clinical results in describing the natural history and time-dependent treatment results of patients suffering from knee OA and should be considered as an additional outcome measure in future studies.

Phytoplankton functional dynamics in a shallow polymictic tropical lake: the influence of emergent macrophytes

This study aimed at investigating the phytoplankton dynamics by employing taxonomic and functional models to test the hypothesis that emergent macrophytes could influence phytoplankton dynamics by increasing the stability of water column and harboring zooplankton. It was also hypothesized that functional models are better than taxonomic approaches to depict phytoplankton community structure in a polymictic tropical lake (Ziway, Ethiopia) with substantial macrophyte cover. Twelve sampling sites, extending from the macrophyte vegetation (Typha latifolia and Phragmites australis) covered littoral part to an open water side of the lake, were monitored monthly (January to August, 2016) for physical, chemical and biological parameters. A total of 93 taxa, distributed among six major taxonomic groups, 14 Reynolds functional groups and six morphology-based functional groups, were identified. The phytoplankton groups, which prefer stable water column and tolerate grazing dominated towards the macrophyte zones, while the phytoplankton capable of surviving strong mixing succeeded towards the completely mixing open water side of the lake. The results of the present study also suggest that the functional classification schemes are robust ways of detecting phytoplankton dynamics along the macrophyte-open water gradient in shallow tropical lakes.

DisProt 7.0: a major update of the database of disordered proteins.

The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.

User difficulties working with a business classification scheme: a case study

Purpose – The purpose of this paper is to provide a unique perspective into user difficulties working with the functional business classification scheme (BCS) to register, search and retrieve corporate information at the Western Australia Police (WA Police). Design/methodology/approach – This paper is a single case study. Questionnaire and interview data were collected and analysed from a sample of ten EDRMS users on their perspectives of working with the BCS. An interpretive analysis methodology was used, and inductive reasoning was used for thematic analysis and sense making of the textual data from the transcripts. Findings – Although the research participants were confident working with the BCS, they reported difficulties finding an appropriate folder that matched the information to be classified and deciding where to file the information. Participants reported that the design and structure of the BCS and training were identified as areas needing improvement. Research limitations/implications – Paradigm shifts in the record-keeping role from the professional to the user may have some bearing on the difficulties users face when dealing with their record-keeping responsibilities. The participants provided comments and suggestions for how to make the BCS more user-friendly, more meaningful and more aligned to the business processes of the users that are practicable and workable solutions for the records professionals to implement. Practical implications – This paper provides a unique user perspective of a BCS, their difficulties working with it and how these difficulties can be resolved in a government organisation. Originality/value – This paper provides a unique user perspective of a BCS, their difficulties working with it and how these difficulties can be resolved in a government organisation.

Knee osteoarthritis functional classification scheme – Validation of time dependent treatment effect. One year follow-up of 518 patients

Objective: The purpose of the current study was to validate time dependent changes of a novel functional classification for patients with knee osteoarthritis (KOA), following a home-based biomechanical treatment (HBBT).Methods: A retrospective analysis of 518 patients with KOA was conducted. All patients were classified using a novel knee osteoarthritis functional grade (KOFG) classification for KOA, based on spatio-temporal gait analysis. Patients were re-classified after 3 months and 1 year of HBBT to examine and validate this classification using timedependant changes. The time dependent changes in the classification were compared to gold-standard selfassessment questionnaires, WOMAC and short form 36 (SF-36).Results: The changes in KOFG were demonstrated over time, with most changes occurring after 3 months of treatment with consolidation of the effect at 12 months. For example, of 427 patients that were classified in KOFG 2-4 grade at baseline, 44.9% and 51.5% had lower (better) KOFG grades at 3 and 12 months of treatment, respectively. The changes in KOFG were validated with WOMAC and SF-36 questionnaires showing a significant correlation between KOFG changes and changes in WOMAC and SF-36. SF-36 pain sub-scale showed an improvement of 33.0% and 38.0% following 3 months and 12 months of treatment, respectively (p values <0.0001).Conclusions: The results of the current study validate the knee osteoarthritis functional grade classification scheme as a tool to assess time dependant changes in KOA as well as its sensitivity to assess treatment effect. The KOFG can offer a more robust mode of reporting clinical results in describing the natural history and time-dependent treatment results of patients suffering from knee OA and should be considered as an additional outcome measure in future studies.

Defining functional groups using dietary data: Quantitative comparison suggests functional classification for seed-dispersing waterfowl

Recent years have seen considerable advances in ecological understanding of the functional role(s) of biodiversity and the connections between biodiversity, ecosystem function and ecosystem service provision. Functional approaches have become important tools for simplifying biodiversity–ecosystem function relationships, but they also have some obvious weaknesses. In particular, since analyses that use functional groups treat members of a group as ecologically interchangeable, functional groups must be defined at a level that simplifies ecological complexity yet retains key ecological distinctions between groups of species. We developed a data-driven approach to functional group definition and applied it to a case study of 16 species of seed-dispersing Afrotropical waterfowl for which we created seed dispersal functional groups using both a priori categories, as typically done in previous studies, and a hierarchical clustering approach. Relevant functional differences and similarities occur among the waterfowl, particularly in the types of plant family dispersed. We found evidence for at least five functional groups of seed disperser. The different groupings have important implications for both wetland and terrestrial plant dispersal. Our analysis suggests that even for a relatively data-scarce study system, using a data-driven approach to generate functional groups offers a feasible and ecologically rigorous approach and is a useful alternative to simple a priori classification schemes. Our approach is capable of capturing variation across several functional traits and suggests that existing datasets may be useful in exploring variation in biodiversity–ecosystem function relationships. Since functional classification schemes may affect our conclusions about biodiversity, ecosystem function and ecosystem service provision, considerable care should be given to ensuring that functional groups are not defined in such a way as to mask important ecological differences among supposedly similar species.

Classification of current scoring functions.

Scoring functions are a class of computational methods widely applied in structure-based drug design for evaluating protein-ligand interactions. Dozens of scoring functions have been published since the early 1990s. In literature, scoring functions are typically classified as force-field-based, empirical, and knowledge-based. This classification scheme has been quoted for more than a decade and is still repeatedly quoted by some recent publications. Unfortunately, it does not reflect the recent progress in this field. Besides, the naming convention used for describing different types of scoring functions has been somewhat jumbled in literature, which could be confusing for newcomers to this field. Here, we express our viewpoint on an up-to-date classification scheme and appropriate naming convention for current scoring functions. We propose that they can be classified into physics-based methods, empirical scoring functions, knowledge-based potentials, and descriptor-based scoring functions. We also outline the major difference and connections between different categories of scoring functions.

In silico characterization of hypothetical proteins from Paracoccidioides lutzii.

Nearly 60% of Paracoccidioides lutzii genes encode products annotated as hypothetical or predicted proteins (HPs). In this study, we describe the global detection and functional inference of HPs, using computational methods based on sequence similarity, identification of targeting signals, presence of known protein domains, and use of the Gene Ontology functional classification scheme. Our analysis enabled a high-throughput characterization of predicted cellular localization and presence of protein domains, clustering HPs into different functional categories including metabolism, localization, cell cycle, response to stimulus, and signaling. To investigate P. lutzii HP expression profiles, we used data obtained from the expressed sequence tag database (dbEST). These analyses revealed 2364 HPs expressed in different situations, namely in mycelial and yeast forms, during the transition from mycelium to yeast, and under conditions mimicking infection. Based on this transcriptomic data, we performed a functional enrichment analysis according to the domains present in the HPs expressed in each condition. The most overrepresented functional domains were those involved in the regulation of gene expression, suggesting important and as yet undescribed roles for these HPs in the adaptation of P. lutzii to environmental conditions. In addition, the expression profiles of six randomly selected HPs were analyzed by quantitative real-time polymerase chain reaction in order to verify their expression in the complementary DNA libraries analyzed in this investigation. The approach used in this study should improve functional characterization of P. lutzii HPs.

Series y subseries en un sistema de clasificación funcional

La generalización de los sistemas de clasificación funcional que se han impuesto en la archivística actual nos demanda el replanteamiento de algunos de los tradicionales conceptos de nuestra disciplina y, en ocasiones, la incorporación de otros relativamente nuevos. La experiencia de los archiveros de la Administración Autonómica de Canarias en la construcción de un cuadro de clasificación funcional para todo el fondo de la Institución nos permite reflexionar sobre la operatividad de los conceptos de “serie genérica” y “subserie”, definidos a partir de una interpretación relativamente flexible del principio de procedencia.

Functional classification scheme for records

PurposeThe purpose of this paper is to present the findings of studies conducted during the period 1986‐2010 in 75 Icelandic organizations on how employees classified or did not classify information and records.Design/methodology/approachA qualitative methodology was used, involving open‐ended interviews, participant observations and internal documentary material.FindingsThe studies revealed that very few of the organizations used a functional classification scheme (FCS) organization‐wide to classify records when the data collection took place. When FCS was not used, records were variably stored unclassified or were classified by the employees according to individualistic schemes made up by themselves. It was further discovered that influential factors in a successful implementation of FCS were user participation in designing FCS, proper training and top management support in its use.Practical implicationsThe findings could be practical for organizations that intend to improve information and records management and to maximize efficient retrieval of records for business and legal purposes. They could be a starting point in successful introduction of FCS in organizations, both in Iceland and abroad.Originality/valueThere is a lack of systematic analysis of studies on classification of records and FCS, not only in Iceland but in other countries as well. The findings provide new knowledge on how employees classify or do not classify records and use or do not use FCS and of which are the most influential factors in a successful implementation of such schemes.

COMPARISON OF CULTURED TRICHODESMIUM (CYANOPHYCEAE) WITH SPECIES CHARACTERIZED FROM THE FIELD(1).

The filamentous, colonial cyanobacterium Trichodesmium has six well-described species, but many more names. Traditional classification was based on field samples using morphological characteristics such as cell width and length, gas vesicle distribution, and colony morphology. We used the Woods Hole Trichodesmium culture collection to identify 21 cultured strains to species using cell morphology; phycobiliprotein absorption spectra; and sequences of the 16S rRNA gene, the 16S-23S internal transcribed spacer (ITS), and the heterocyst differentiation gene hetR. We compared our results to previous studies of field specimens and found similar clades, though not all phylogenetic groups were represented in culture. Our culture collection represented two of the four major clades of Trichodesmium: clade I, made up of Trichodesmium thiebautii Gomont, Trichodesmium tenue Wille, Katagnymene spiralis Lemmerm., and Trichodesmium hildebrandtii Gomont; and clade III, consisting of Trichodesmium erythraeum Ehrenb. and Trichodesmium contortum Wille. These clades were genetically coherent with similar phycobiliprotein composition, but morphologically diverse. In the continual revision of cyanobacterial taxonomy, genetic and biochemical information is useful and informative complements to morphology for the development of a functional classification scheme.

Functional classification of records and organisational structure

PurposeThis paper seeks to examine how an electronic records management system has been used in a Finnish government agency. In particular, it aims to study the relationship between functional classification scheme and the way users in different organisational units and at different organisational levels have employed the system. The goal is to examine whether electronic records management systems were easier to use if the system “knew” what functional classes the user (or other employees in the user's organisational unit) typically need in their work.Design/methodology/approachThe study is based on two sources. The first source is metadata in records that were captured in the electronic records management system of the agency. It reflects actual behaviour of users when they interact with the system and classification of records. The second source is distribution of functions to organisational units in the light of policy documents and a survey made in the organisation. The study compares the two sources to see how the users have employed the electronic records management system in their work and how this relates to organisational structure and supposed usage of the system.FindingsIn general, individual employees employ only a small part of the classification. However, this does not apply at a higher level in the organisational hierarchy: the higher the person's position in the hierarchy, the more classes he/she is likely to use in the work. Regardless of the position, the classes are generally those identified as belonging to the employee's unit.Research limitations/implicationsThe study is based on one agency with a functional organisational structure. The findings may not apply to organisations where job descriptions are fluid. They should also be tested in more complex organisational settings. One could develop new methods of automated classification which combine analysis of document content with contextual reasoning about the likely functional classes.Practical implicationsAccess to electronic records management systems could be facilitated by creating in systems user/unit profiles defining what functional classes the user is most likely to need in their work. It would also be useful if systems simply remembered what functional classes the user has needed in the past.Originality/valueThe study offers insight into how an electronic records management system is used in an organisation. This is valuable for companies developing records management software and persons trying to gain a deeper understanding of records management in organisations.

PS190. The Role of Magnetic Resonance Imaging and a Functional Classification Scheme in the Diagnosis and Management of Patients with Vascular Malformations

PS190. The Role of Magnetic Resonance Imaging and a Functional Classification Scheme in the Diagnosis and Management of Patients with Vascular Malformations

Unveiling protein functions through the dynamics of the interaction network.

Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.